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The epigenome regulates transcription of target genes through DNA methylation- or histone methylation/acetylation/phosphorylation/ubiquitination-mediated alteration of genomic function or chromatin conformation. Recent genomic studies have shown that multiple genes encoding epigenetic regulators are frequently and recurrently mutated in MDS, suggesting that epigenetic dysregulation is significantly associated with the molecular pathogenesis and clinical features of MDS. In this review, we will present our recent findings together with others, focusing on physiological molecular functions of epigenetic regulators recurrently mutated in MDS and on functional correlation between dysregulated epigenomic regulators and molecular pathogenesis/clinical features of MDS.

The epigenome can adequately regulate the on/off states of genes in response to external environmental factors and stress. In recent years, it has been observed that the epigenome, which is modulated through DNA methylation, histone modifications, and chromatin remodeling, changes with age. Alterations in the epigenome lead to the loss of cell-specific epigenome/identity, which in turn triggers a decline in tissue function. In mammals, postnatal epigenomic variations are not only caused by metabolic diseases, such as diabetes or DNA damage, but also by social stress and infectious diseases. Unlike Genome-Wide Association Studies (GWAS), dynamically changing epigenomes, along with their cellular roles, need to be established as objective biomarkers in conjunction with various biological signals, such as walking speed, brain waves, and clinical data. The biological age/aging clock, determined by methylated DNA, has attracted attention, and calorie restriction not only slows the progression of aging, but also seems to suppress it. However, as indicated by gene expression analysis in aging mice, aging is not a linear model, but is represented by nonlinear dynamic changes. Consequently, the development of experimental models and analytical methods that enhance temporal resolution through time-series analysis, tailored to spatial resolution, such as cell distribution and organ specificity, is progressing. Moreover, in recent years, in addition to anti-aging efforts targeting epigenomic variations, global attention has increasingly focused on research and development aimed at rejuvenating treatments, thus leading to the birth of many biotech companies. Aging Hallmarks such as inflammation, stem cells, metabolism, genomic instability, and autophagy, interact closely with the epigenome. Various postnatal and reversible epigenomic controls of aging, including Yamanaka factors (OKSM and OSK), are now entering a new phase. In the future, the development of aging control using diverse modalities, such as mRNA, artificial peptides, and genome editing, is expected, along with an improved molecular understanding of aging and identification of useful biomarkers.

Malignant lymphomas are a group of diseases in which epigenomic abnormalities are fundamental to the pathogenesis and pathophysiology and are characterized by a high frequency of abnormalities in DNA methylation regulators and histone modifiers. These epigenomic abnormalities directly amplify malignant clones. They also originated from a cell lineage differentiated from hematopoietic stem cells through epigenomic changes. These characteristics are associated with their high affinity for epigenomic therapies. Hematology has been a leader in the basic, clinical, and drug discovery areas of disease epigenetics. However, the epigenomic regulation is generally recognized as a complex system, and gaps are observed between basic and clinical studies. To overview the status and importance of "epigenomic abnormalities in malignant lymphoma," this review first summarizes the concept and essential importance of the epigenome and then outlines the current status and future perspective of epigenomic abnormalities in malignant lymphomas.

Recent progress in whole genome sequencing has identified recurrent somatic mutations in the additional sex combs like 1 (ASXL1) gene in a variety of hematological disorders and even in premalignant conditions. However, the molecular mechanisms regarding the contribution of ASXL1 mutation to the pathogenesis of premalignant conditions remain largely unelucidated. Thus, we investigated the biological effects of mutant Asxl1 using newly-generated knock-in (KI) mice. Heterozygous mutant KI mice developed phenotypes resembling human low-risk myelodysplastic syndromes (MDS), and some of them developed an MDS/myeloproliferative neoplasm-like disease after a long latency. The H2AK119ub1 level around the promoter region of p16 Ink4a was significantly decreased in KI hematopoietic stem cells (HSCs), suggesting perturbation of Bmi1-driven H2AK119ub1 histone modification by mutant Asxl1. The mutant Asxl1 failed to interact with Bmi1, although wild type ASXL1 protein did not. When p16 Ink4a expression was depleted in Asxl1 KI mice, the HSC pool was restored, and apoptosis was ameliorated in HSCs. These findings demonstrate that the loss of protein interaction between mutant Asxl1 and Bmi1 affected the activity of Prc1. The subsequent derepression of p16 Ink4a by aberrant histone ubiquitination could induce cellular senescence, resulting in low-risk MDS-like phenotypes in heterozygous Asxl1 KI mice.

Histone H3 lysine 27 tri-methylation (H3K27me3) -dependent transcription regulation is a fundamental process of gene control. Although EZH2 mutation is observed in certain lymphoma types, many other cancers show global H3K27me3 accumulation irrespective of mutation. However, the underlying mechanisms of gene silencing and therapeutic efficacies of epigenetic drugs remain unclear. In this study, we showed that globally-accumulated H3K27me3 is induced by both cis-bound EZH1 and EZH2 in mature lymphocyte-derived malignancies. Mutual interference and compensatory functions of co-expressed EZH1/2 rearrange the genome-wide distribution, establishing restricted chromatin and gene expression signatures. Using novel EZH1/2 dual inhibitors, we found that both EZH1 and EZH2 are required for the maintenance and induction of H3K27me3. The synthetic lethality of targeting EZH1 and EZH2 was observed in lymphoma models and primary adult T-cell leukemia/lymphoma (ATL) cells harboring H3K27me3 accumulation. This heritable EZH1/2 dysfunctional state was epigenetically imprinted at the virus-infected, immortalized phase. EZH1/2 dual inhibition could eliminate infected cell populations more effectively than EZH2 inhibition. Regarding the frequent observation of H3K27me3 accumulation in advanced-stage and early-phase malignant progenitors, the emerging EZH1- and EZH2-dependent epigenetic reprograming is an incipient process of fate decision within developmental pathways of cancers.

Epigenetic alterations, represented byaberrant DNA methylation, are present in gastrointestinal cancers. Detection of cancer- specific DNA methylation can be used to detect cancer, and detection of colon cancer-specific aberrant DNA methylation is alreadyapproved byFDA. Aberrant DNA methylation is potentlyinduced bychronic inflammation, and also is accumulated in normal tissues before a cancer develops. In gastric cancer, potential of cancer risk diagnosis bymeasurement of aberrant DNA methylation in normal gastric mucosae has been clinically demonstrated. Therapeutically, DNA demethylating agents have been alreadyapproved for hematological tumors byFDA, and promising results in clinical trials against gastrointestinal cancers have been reported. Also, histone deacetylase inhibitors have been already approved for hematological tumors, and clinical trials against gastrointestinal cancers have been reported. Selection of right dose, schedule, combination, and patients is the keyto future success.

Epigenetic regulation holds a key role in gene expression due to its modulation of the structure and function of chromatin. Notably, epigenetic dysregulation is deeply involved in the pathogenesis of hematological malignancies. Polycomb group (PcG) genes encoding histone modifier proteins are representative epigenetic genes that regulate a variety of cellular functions, including self-renewal and multi-lineage differentiation of stem cells. Surprisingly, many PcG genes are targeted by deletions or somatic mutations or both in a number of hematological malignancies, such as myelodysplastic syndrome (MDS). PcG proteins form multiprotein complexes and exert either oncogenic or tumor-suppressive functions, depending on the tumor type. In MDS, they function as tumor suppressors. This review summarizes the current knowledge on deregulated polycomb function in the pathogenesis of MDS.

Epigenetic regulation underlying AR(Androgen receptor)mediated transcription is important component to understand pathophysiology of osteoporosis in men. In this commentary, it is reported recent findings related to epigenetic landscape governed by AR and its cofactors including lysine-specific demethylase 1 (LSD1), and possible implication for bone metabolism.

The importance of receptor activator of nuclear factor-κB ligand(RANKL)during osteoclastogenesis was discovered in 1998. After that Nfatc1, downstream gene of RANKL-RANK signaling, was identified as a master regulator of osteoclastogenesis by transcriptome analysis. In recent years, with the advancement of epigenetic analysis method and big data analysis technology, epigenetic analysis about osteoclastogenesis gradually progresses. Some papers using H3K4me3 and H3K27me3 histone modification change data, DNase-seq data and formaldehyde-assisted isolation of regulatory elements(FAIRE)-seq data during osteoclastogenesis were published recently. It will probably contribute to elucidate the crosstalk between osteoclasts and osteoblasts, osteocytes or chondrocytes in the future.

Epigenetic marks, such as histone modifications or DNA methylation, regulate tissue specific gene expression by affecting the structures and accessibility of chromatin or DNA. Epigenetics, the molecular mechanisms regulating the epigenome, would therefore be critically involved in development and cell differentiation versus proliferation. Histone modifications include methylation, acetylation, phosphorylation and ubiquitination of specific lysine, arginine or serine residues on histone tails, and each modification has its own specific effect on gene expressions. Modification of histones is accomplished by multimeric protein complexes including polycomb and trithorax group proteins. Regulation of DNA methylation is another mechanism of epigenetic regulation, which is achieved by DNA methyltransferase (DNMT) and TET family proteins. Methylation of cysteine residues on DNA generally leads to transcriptional repression, and oxidation of methylated cysteines provides another type of molecular mark on DNA that regulates gene expression. Next generation sequencing of tumor genomes has uncovered recurrent somatic mutations of epigenetic genes such as DNMT3A, TET2, and ASXL1 in hematologic malignancies, showing that epigenetic dysregulation is a critical step leading to the transformation of hematopoietic cells. Rigorous integrated functional analyses of mutated epigenetic genes are currently underway, and are anticipated to lead to the development of novel molecularly targeted therapies for hematologic malignancies.

Cumulative evidence suggests that at least some hematologic malignancies are derived from alterations of epigenetic machinery. Next generation sequencing has revealed recurrent mutations of genes related to DNA methylation and histone modification in myelodysplastic syndromes (MDS), acute myeloid leukemia, malignant lymphoma, and multiple myeloma. Both these pathways are targetable and specific inhibitors of their related proteins are currently in development. Among these novel therapies, hypomethylating agents have been approved for MDS, and recently, histone deacetylase inhibitors became available for T-cell lymphoma and multiple myeloma. Agents currently undergoing clinical trials include inhibitors of IDH2 targeting DNA methylation, and EZH2, Dot1L, and BRD4 inhibitors designed to target either writers or readers of post-translational modifications (PTMs) of histones. In a phase I setting, where the maximum tolerated dose has not been reached, efficacy was reported with these agents. Furthermore, Dot1bL and IDH2 inhibitors have been shown to induce differentiation of leukemic blasts in patients with MLL gene rearrangements and IDH2 mutations, respectively, thus providing functional evidence supporting the use of inhibitors of epigenetic mechanisms as a means of differentiation therapy for hematologic malignancies.

Cancer is known to be a genetic disease, which is caused by abnormalities of oncogenes and/or tumor-suppressor genes. Genetic abnormalities include mutation, deletion or amplification of DNA sequences. Based on the findings of the genetic abnormalities in malignant tumors, many molecular-targeting agents, e.g. Bcr-Abl kinase inhibitors and EGFR kinase inhibitors, have been developed and approved. In addition to genetic abnormalities, epigenetic abnormalities, e.g. DNA methylation, histone methylation and histone acetylation, are also involved in carcinogenesis and tumor development. Based on the findings of the epigenetic abnormalities in malignant tumors, the novel epigenetic molecular-targeting agents, e.g. DNA(DNMT) methyltransferase inhibitors and histone deacetylase (HDAC) inhibitors, have also been developed and approved. Moreover, histone methyltransferase(HMT) inhibitors and histone demethylase(HDM) inhibitors have been also discovered and some agents are in clinical trials.

Epigenetic abnormalities are central players in the disruption of common cancer pathway, and epigenetic aberrations have also been shown to play an important role in development of multiple myeloma. DNA methylation, histone modifications contribute to the pathogenesis of multiple myeloma. Understanding of epigenetic abnormalities in myeloma leads to development of novel drugs such as histone deacetylase inhibitors (HDACi). Here I will discuss about common epigenetic mechanisms (aberrant DNA methylation, histone modifications), the epigenetic aberrations in myeloma and clinical development of novel drug HDACi.

Increasing evidence has demonstrated that chronic hypoxia in the tubulointerstitium results in irreversible chronic kidney diseases. Hypoxia inducible factor (HIF) is a transcriptional master regulator which takes control of gene expressions under hypoxia. Recently, HIF1 has been reported to organize a cluster of histone-modifying enzymes by binding to their promoter regions in various kinds of cell line. In order to clarify the epigenetic molecular mechanisms by HIF1, we examined the genome-wide analysis of HIF1-binding sites (ChIP-seq) in endothelial cells and HIF1 downstream target genes using DNA microarrays. ChIP-seq results demonstrated that HIF1 binds to the enhancer regions in addition to the promoter regions. We clarified that one of the HIF1 downstream genes, SLC2A3 (solute-carrier family 2A3, also known as glucose transporter 3: GLUT3), is regulated by changing chromosomal conformations under hypoxia via a cooperative combination of HIF1 and KDM3A(lysine(K) specific demethylase 3A), one of the histone demethylases. KDM3A is recruited to the SLC2A3 loci in an HIF1-dependent manner and demethylates histone repressive mark, H3K9me2, up-regulating its expression. In addition, we confirmed the interactions of HIF1 and KDM3A only under hypoxia using co-immunoprecipitation. These experimental results showed novel HIF1-dependent molecular mechanisms from an epigenetic viewpoint. It is important to elucidate the epigenetic mechanisms of chronic hypoxia in order to identify novel therapeutic approaches against chronic kidney disease.

Epigenetic therapy is highly anticipated as a next player to molecular target drugs. Epigenetic abnormalities are maintained even after a somatic cell division, and can be causally involved in carcinogenesis. Recent cancer genome analysis revealed that a significant fraction of cancers cannot be accounted for only by mutations of known protein-coding genes, and that mutations of epigenetic genes are unexpectedly frequent. DNA demethylating drugs and histone deacetylase inhibitors are already approved, and many next-generation epigenetic drugs are under development. Application of epigenetic therapies to solid tumors is being attempted, and a promising result is available for non-small cell lung cancers. Right patients, right doses, and right combinations are key to further success, and can be done based on recent progresses in mechanistic analyses.

Recent research has demonstrated that complex 'epigenetic' mechanisms, which regulate gene transcription without altering the DNA code, could play a critical role in the pathophysiology of psychiatric disorders. We previously reported that pretreatment of mice with 5-HT(1A) receptor agonists 24 hr before testing suppressed the decrease in emotional behaviors induced by exposure to acute restraint stress. In addition, DNA microarray analysis showed that such a pretreatment with 5-HT(1A) receptor agonist produces changes in several gene transcriptions in the hippocampus including the reduction of histone deacetylase 10. Based on these findings, we recently carried out studies focused on the relationship between the development of emotional resistance to stress and histone acetylation induced by a 5-HT(1A) receptor agonist as well as a histone deacetylase inhibitor. The findings suggest that 5-HT(1A) receptor agonists may be useful for preventing mental illnesses that arise due to a decreased resistance and adaptability to stress. Moreover, the notion that chromatin remodeling is an important mechanism in mediating emotionality under stressful situations is further supported.

Osteoclasts are multinuclear fusion cells derived from monocyte and macropharge lineage cells, which are differentiated in the presence of M-CSF and RANKL. Some transcription factors, such as NFATc1, are known to be associated with osteoclastogenesis however, the epigenetic regulation is not uncovered. Recently it was revealed that the activation and the repression of gene in the ES cells were strictly regulated by the histone modification, such as H3K4/H3K27 trimethylation mark. In this section we review the epigenetic regulation by histone modification and the role in osteoclastogenesis.

Androgen and estrogen are sex steroid hormones, which bind to it own nuclear receptors, such as androgen receptor (AR) and estrogen (ER) , and exert its action through regulation of target gene expressions, and contribute to the maintenance of various homeostasis. However, the mode of binding of AR and ER binding site on the genome DNA and their intracellular behavior are diverse in various cells. From genome-wide analysis studies with the advent and remarkable development of next-generation sequencer in recent years, it has been clarified that new features and mechanism of action of sex hormone receptors in breast cancer and prostate cancer. In this paper, we focus on the AR, together with recent findings on genome-wide analysis, and we also introduce the current application for bone metabolism.

Evidence including genome-wide analyses have uncovered that epigenetic mechanisms regulate differentiation and effector functions in CD8 T cells. Gene expression profiles change when CD8 T cells differentiate from naïve T cells to memory T cells. It has been shown that this programmed differentiation is regulated by epigenetic mechanisms. Upon antigen stimulation, CD8 T cells activate and acquire effector functions to target cells. Effector molecule gene expressions are upregulated by epigenetic mechanisms in CD8 T cells. It is suggested that memory T cells respond more rapidly to antigens because chromatin structures of effector molecule genes are open and their gene transcriptions are poised for activation.

Epigenetics mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in normal cells. Certain forms of histone methylation induce local heterochromatin formation, which is readily reversible, whereas DNA methylation leads to stable long-term repression. The precise epigenomic landscape present in normal cells undergoes extensive distortion in cancer. These characteristic epigenetic mechanisms are thought to be associated with tumor formation and progression. The reversible nature of epigenetic changes has led to the emergence of the field of epigenetic therapy, which may lead to potent and promising cancer treatment.

Epigenetic modifications, involving DNA methylation and histone modifications, are maintained upon somatic cell replication, and are fundamental mechanisms for cellular memory. DNA methylation of promoter CpG islands of tumor-suppressor genes can silence their downstream genes, and can be causally involved in cancer development and progression. Since this effect is the same with that of inactivating mutations, the natures of DNA methylation were once considered to be similar to mutations. However, recently, it was revealed that a large number of epigenetic alterations are present in a single cancer cell, that a large number of cells have an epigenetic alteration of a specific gene in non-cancerous, thus polyclonal, tissues, that gene specificity in methylation induction is present according to tissue types and inducers, and that chronic inflammation is deeply involved in methylation induction. These facts suggest that epigenetic alterations of key genes involved in acquired chronic disorders can be present in a significant fraction of cells in a tissue, and thus can impair the function of the tissue. Associations between epigenetic alterations and behavior, memory, mental disorders, neurological disorders, metabolic disorders, allergy, autoimmune disorders, and other disorders have been reported. Further research in the field is necessary to clarify the causal roles of these epigenetic alterations in disease development, and to apply the findings to new strategies of disease prevention, diagnosis, and treatment.