Polycomb Group Target Research Articles

Dynamics of H3K4me3 Chromatin Marks Prevails over H3K27me3 for Gene Regulation during Flower Morphogenesis in Arabidopsis thaliana

Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes (trxG), respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related Histone 3 trimethylation at lysine 4 (H3K4me3). However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with expression changes, in a developmental series including Arabidopsis thaliana leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prevail over changes in H3K27me3 and quantitatively correlate with expression changes, while H3K27me3 changes occur later. Notably, we found that H3K4me3 increase during the early activation of PcG target genes while H3K27me3 level remain relatively constant at the locus. Our results reveal that H3K4me3 predicts changes in gene expression better than H3K27me3, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation

Master regulatory genes require stable silencing by the polycomb group (PcG) to prevent misexpression during differentiation and development. Some PcG proteins covalently modify histones, which contributes to heritable repression. The role for other effects on chromatin structure is less understood. We characterized the organization of PcG target genes in ESCs and neural progenitors using 5C and super-resolution microscopy. The genomic loci of repressed PcG targets formed discrete, small (20-140 Kb) domains of tight interaction that corresponded to locations bound by canonical polycomb repressive complex 1 (PRC1). These domains changed during differentiation as PRC1 binding changed. Their formation depended upon the Polyhomeotic component of canonical PRC1 and occurred independently of PRC1-catalyzed ubiquitylation. PRC1 domains differ from topologically associating domains in size and boundary characteristics. These domains have the potential to play a key role in transmitting epigenetic silencing of PcG targets by linking PRC1 to formation of a repressive higher-order structure.

Dietary phytochemical PEITC restricts tumor development via modulation of epigenetic writers and erasers

Dietary intake of bioactive phytochemicals including the cruciferous vegetable derivative phenethyl isothiocyanate (PEITC) can reduce risk of human cancers, but possible epigenetic mechanisms of these effects are yet unknown. We therefore sought to identify the molecular basis of PEITC-mediated epigenetic tumor restriction. Colon cancer cells treated with low-dose PEITC for >1 month exhibited stable alterations in expression profile of epigenetic writers/erasers and chromatin-binding of histone deacetylases (HDACs) and Polycomb-group (PcG) proteins. Sustained PEITC exposure not only blocked HDAC binding to euchromatin but was also associated with hypomethylation of PcG target genes that are typically hypermethylated in cancer. Furthermore, PEITC treatment induced expression of pro-apoptotic genes in tumor cells, which was partially reversed by overexpression of PcG member BMI-1, suggesting opposing roles for PEITC and PcG proteins in control of tumor progression. These data demonstrate that PEITC regulates chromatin binding of key epigenetic writers/erasers and PcG complexes to restrict tumor development.

PHF19 Promotes Drug Resistance through EZH2 Inactivation in Multiple Myeloma

Background: Multiple myeloma (MM) is a plasma cell malignancy characterized by mass growth of clonal plasma cells in the bone marrow, the secretion of abnormal monoclonal immunoglobulins and lytic bone lesions. Although current therapies have improved the outcome of patients, MM remains an incurable disease with a high rate of relapse and refractory. The survival of MM patients ranged from less than one month to more than 10 years. MM cells survival are more dependent on bone marrow microenvironment which induced drug-resistance of anti-MM agents. Cytogenetic aberrations of MM cell, such as chromosomal translocation, deletion and amplification induced oncogenes activation and tumor suppressor genes inactivation. Furthermore, epigenetic changes, such as histone methylation, have been suggested as a mediation of chemotherapy resistance in several cancer types, including MM. PcG (Polycomb group) proteins are conserved transcriptional repressors and essential to regulate cell fate.There were two main families of chromatin-modifying complexes, PRC1 (Polycomb repressive complex 1) and PRC2-4. In Drosophila, PRC2 contains the H3K27 histone methytransferase E (Z) whose trimethylation activity towards PcG target genes is stimulated by PCL (polycomb-like) protein. Three PCL paralogues have been identified: PHF1, MTF2 and PHF19. In this study, we found out that PHF19 is overexpressed and was related with relapse and drug resistance in multiple myeloma.Materials and methods: Gene Expression Profile Assay (GEP) was conducted in sequential patient samples including newly diagnosed, post-treatment and relapsed. 51 newly diagnosed and relapsed paired samples, 19 newly diagnosed and post-treatment paired specimens, 9 patients have newly diagnosed, post-treatment and relapsed samples at different time points were elucidated in this study. MM relapsed and drug-resistance highly correlated genes were screened and the prognosis and survival analysis were conducted. Real time quantitative PCR (RQ-PCR) and Western blotting were used to analysis the expression of the gene in MM cell lines and MM patients. The candidate gene was overexpressed in MM cells by lentiviral infection. The cell proliferation and drug sensitivity of MM cells and proteins in correlated signaling pathways were detected.Results: GEP assay showed that 56 genes expression in MM resistant clones after treatment and relapse have significantly increased, with 20 genes closely associated with the poor prognosis. Among them, PHF19, a component of the Polycomb repressive complex 2 (PRC2) family,significantly increased in relapsed and refactory patients and myeloma cell lines.The progression-free survival (PFS) and overall survival (OS) were significantly shortened in MM patients with overexpressed PHF19. PHF19 overexpression (OE) promoted the proliferation and inhibited apoptosis of MM cells. The sensitivity to doxorubicin and vincristine was significantly reduced in the PHF19 OE cells. Western blotting showed that the phosphorylation of EZH2 was significantly increased in PHF19 OE cells, while H3K27me3 level was significantly down-regulated. Overexpressed PHF19 through activating NF-κB signaling pathway induced persistent expression of EZH2 and their downstream anti-apoptotic gene, such as IGF1, BCL2 and HIF1α, which induced cell proliferation and drug resistance. Thus targeting PHF19, inhibiting the phosphorylation of EZH2 and sustaining histone H3K27 methylation level may be a potential therapeutic target in relapsed or refractory myeloma patients.Conclusions: PHF19 expression was obviously increased in MM relapse and drug resistance patients with poor prognosis. Inhibition PHF19 and counteraction EZH2 phosphorylation should be combined to improve chemotherapy induced hypermethylation of H3K27, which may be a new therapeutic strategies in relapsed or refractory myeloma. DisclosuresNo relevant conflicts of interest to declare.

RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes

Polycomb group (PcG) proteins function as chromatin-based transcriptional repressors that are essential for normal gene regulation during development. However, how these systems function to achieve transcriptional regulation remains very poorly understood. Here, we discover that the histone H2AK119 E3 ubiquitin ligase activity of Polycomb repressive complex 1 (PRC1) is defined by the composition of its catalytic subunits and is highly regulated by RYBP/YAF2-dependent stimulation. In mouse embryonic stem cells, RYBP plays a central role in shaping H2AK119 mono-ubiquitylation at PcG targets and underpins an activity-based communication between PRC1 and Polycomb repressive complex 2 (PRC2) which is required for normal histone H3 lysine 27 trimethylation (H3K27me3). Without normal histone modification-dependent communication between PRC1 and PRC2, repressive Polycomb chromatin domains can erode, rendering target genes susceptible to inappropriate gene expression signals. This suggests that activity-based communication and histone modification-dependent thresholds create a localized form of epigenetic memory required for normal PcG chromatin domain function in gene regulation.

Correlation of an epigenetic mitotic clock with cancer risk.

BackgroundVariation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be influenced by extrinsic factors which modulate this rate of stem cell division. To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk.ResultsHere, we integrate mathematical modeling with prior biological knowledge to construct a DNA methylation-based age-correlative model which approximates a mitotic clock in both normal and cancer tissue. By focusing on promoter CpG sites that localize to Polycomb group target genes that are unmethylated in 11 different fetal tissue types, we show that increases in DNA methylation at these sites defines a tick rate which correlates with the estimated rate of stem cell division in normal tissues. Using matched DNA methylation and RNA-seq data, we further show that it correlates with an expression-based mitotic index in cancer tissue. We demonstrate that this mitotic-like clock is universally accelerated in cancer, including pre-cancerous lesions, and that it is also accelerated in normal epithelial cells exposed to a major carcinogen.ConclusionsUnlike other epigenetic and mutational clocks or the telomere clock, the epigenetic clock proposed here provides a concrete example of a mitotic-like clock which is universally accelerated in cancer and precancerous lesions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1064-3) contains supplementary material, which is available to authorized users.

The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation.

There is a growing perception that long non-coding RNAs (lncRNAs) modulate cellular function. In this study, we analyzed the role of the lncRNA HOTAIR in mesenchymal stem cells (MSCs) with particular focus on senescence-associated changes in gene expression and DNA-methylation (DNAm). HOTAIR binding sites were enriched at genomic regions that become hypermethylated with increasing cell culture passage. Overexpression and knockdown of HOTAIR inhibited or stimulated adipogenic differentiation of MSCs, respectively. Modification of HOTAIR expression evoked only very moderate effects on gene expression, particularly of polycomb group target genes. Furthermore, overexpression and knockdown of HOTAIR resulted in DNAm changes at HOTAIR binding sites. Five potential triple helix forming domains were predicted within the HOTAIR sequence based on reverse Hoogsteen hydrogen bonds. Notably, the predicted triple helix target sites for these HOTAIR domains were also enriched in differentially expressed genes and close to DNAm changes upon modulation of HOTAIR. Electrophoretic mobility shift assays provided further evidence that HOTAIR domains form RNA–DNA–DNA triplexes with predicted target sites. Our results demonstrate that HOTAIR impacts on differentiation of MSCs and that it is associated with senescence-associated DNAm. Targeting of epigenetic modifiers to relevant loci in the genome may involve triple helix formation with HOTAIR.

H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system.

Polycomb group (PcG) proteins form an epigenetic memory system in plants and animals, but interacting proteins are poorly known in plants. Here, we have identified Arabidopsis UBIQUITIN SPECIFIC PROTEASES (USP; UBP in plant and yeasts) 12 and 13 as partners of the plant-specific PcG protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). UBP12 binds to chromatin of PcG target genes and is required for histone H3 lysine 27 trimethylation and repression of a subset of PcG target genes. Plants lacking UBP12 and UBP13 developed autonomous endosperm in the absence of fertilization. We have identified UBP12 and UBP13 as new proteins in the plant PcG regulatory network. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. We have found that Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, we demonstrate that USP7-like proteins are essential for gene silencing in diverse genomic contexts.

Stuxnet Facilitates the Degradation of Polycomb Protein during Development

Polycomb-group (PcG) proteins function to ensure correct deployment of developmental programs by epigenetically repressing target gene expression. Despite the importance, few studies have been focused on the regulation of PcG activity itself. Here, we report a Drosophila gene, stuxnet (stx), that controls Pc protein stability. We find that heightened stx activity leads to homeotic transformation, reduced Pc activity, and de-repression of PcG targets. Conversely, stx mutants, which can be rescued by decreased Pc expression, display developmental defects resembling hyperactivation of Pc. Our biochemical analyses provide a mechanistic basis for the interaction between stx and Pc; Stx facilitates Pc degradation in the proteasome, independent of ubiquitin modification. Furthermore, this mode of regulation is conserved in vertebrates. Mouse stx promotes degradation of Cbx4, an orthologous Pc protein, in vertebrate cells and induces homeotic transformation in Drosophila. Our results highlight an evolutionarily conserved mechanism of regulated protein degradation on PcG homeostasis and epigenetic activity.

The cohesin-associated protein Wapal is required for proper Polycomb-mediated gene silencing.

BackgroundThe cohesin complex consists of multiple core subunits that play critical roles in mitosis and transcriptional regulation. The cohesin-associated protein Wapal plays a central role in off-loading cohesin to facilitate sister chromatid separation, but its role in regulating mammalian gene expression is not understood. We used embryonic stem cells as a model, given that the well-defined transcriptional regulatory circuits were established through master transcription factors and epigenetic pathways that regulate their ability to maintain a pluripotent state.ResultsRNAi-mediated depletion of Wapal causes a loss of pluripotency, phenocopying loss of core cohesin subunits. Using chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq), we determine that Wapal occupies genomic sites distal to genes in combination with CTCF and core cohesin subunits such as Rad21. Interestingly, genomic sites occupied by Wapal appear enriched for cohesin, implying that Wapal does not off-load cohesin at regions it occupies. Wapal depletion induces derepression of Polycomb group (PcG) target genes without altering total levels of Polycomb-mediated histone modifications, implying that PcG enzymatic activity is preserved. By integrating ChIP-seq and gene expression changes data, we identify that Wapal binding is enriched at the promoters of PcG-silenced genes and is required for proper Polycomb repressive complex 2 (PRC2) recruitment. Lastly, we demonstrate that Wapal is required for the interaction of a distal cis-regulatory element (CRE) with the c-Fos promoter.ConclusionsCollectively, this work indicates that Wapal plays a critical role in silencing of PcG target genes through the interaction of distal CREs with promoters.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0063-7) contains supplementary material, which is available to authorized users.

Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes.

In multicellular organisms, Polycomb Repressive Complex 1 (PRC1) and PRC2 repress target genes through histone modification and chromatin compaction. Arabidopsis thaliana mutants strongly compromised in the pathway cannot develop differentiated organs. LIKE HETEROCHROMATIN PROTEIN1 (LHP1) is so far the only known plant PRC1 component that directly binds to H3K27me3, the histone modification set by PRC2, and also associates genome-wide with trimethylation of lysine 27 of histone H3 (H3K27me3). Surprisingly, lhp1 mutants show relatively mild phenotypic alterations. To explain this paradox, we screened for genetic enhancers of lhp1 mutants to identify novel components repressing target genes together with, or in parallel to, LHP1. Two enhancing mutations were mapped to TELOMERE REPEAT BINDING PROTEIN1 (TRB1) and its paralog TRB3. We show that TRB1 binds to thousands of genomic sites containing telobox or related cis-elements with a significant increase of sites and strength of binding in the lhp1 background. Furthermore, in combination with lhp1, but not alone, trb1 mutants show increased transcription of LHP1 targets, such as floral meristem identity genes, which are more likely to be bound by TRB1 in the lhp1 background. By contrast, expression of a subset of LHP1-independent TRB1 target genes, many involved in primary metabolism, is decreased in the absence of TRB1 alone. Thus, TRB1 is a bivalent transcriptional modulator that maintains downregulation of Polycomb Group (PcG) target genes in lhp1 mutants, while it sustains high expression of targets that are regulated independently of PcG.

Methylation of the Tumor Suppressor Genes HIC1 and RassF1A Clusters Independently From the Methylation of Polycomb Target Genes in Colon Cancer.

Methylation changes within tumor suppressor (TS) genes or polycomb group target (PcG) genes alter cell fates. Chromatin associated with PcG targets is bivalent in stem cells, while TS genes are not normally bivalent. PcG target methylation changes have been identified in tumor stem cells, and abnormal methylation is found in TS genes in cancers. If the epigenetic states of genes influence DNA methylation, then methylation of PcG targets and TS genes may evolve differently during cancer development. More importantly, methylation changes may be part of a sequence in tumorigenesis. Chromatin and methylation states of 4 PcG targets and 2 TS genes were determined in colon cancer cells. The methylation states were also detected in 100 pairs of colon cancer samples. Principle component analysis (PCA) was used to reveal whether TS methylation or PcG methylation was the main methylation change associated with colon cancers. Chromatin and methylation states differ in colon cancer cell lines. The methylation states within PcG targets clustered independently from the methylation states in TS genes, a finding we previously reported in liver cancers. PCA in colon cancers revealed the strongest association with methylation changes in 2 TS genes, HIC1 and RassF1A. Loss of HIC1 methylation correlated with decreased tumor migration. PcG and TS methylation states cluster independently from each other. The deduced principle component correlated better with TS methylation than PcG methylation in colon cancer. Abnormal methylation changes may represent a sequential biomarker profile to identify developing colon cancer.

Kicking against the PRCs - A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2.

The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and consequently trxG mutants suppress PcG mutant phenotypes. We previously identified the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene as a genetic suppressor of mutants in the Arabidopsis PcG gene LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Here, we show that ALP1 interacts genetically with several other PcG and trxG components and that it antagonizes PcG silencing. Transcriptional profiling reveals that when PcG activity is compromised numerous target genes are hyper-activated in seedlings and that in most cases this requires ALP1. Furthermore, when PcG activity is present ALP1 is needed for full activation of several floral homeotic genes that are repressed by the PcG. Strikingly, ALP1 does not encode a known chromatin protein but rather a protein related to PIF/Harbinger class transposases. Phylogenetic analysis indicates that ALP1 is broadly conserved in land plants and likely lost transposase activity and acquired a novel function during angiosperm evolution. Consistent with this, immunoprecipitation and mass spectrometry (IP-MS) show that ALP1 associates, in vivo, with core components of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a widely conserved PcG protein complex which functions as a H3K27me3 histone methyltransferase. Furthermore, in reciprocal pulldowns using the histone methyltransferase CURLY LEAF (CLF), we identify not only ALP1 and the core PRC2 components but also plant-specific accessory components including EMBRYONIC FLOWER 1 (EMF1), a transcriptional repressor previously associated with PRC1-like complexes. Taken together our data suggest that ALP1 inhibits PcG silencing by blocking the interaction of the core PRC2 with accessory components that promote its HMTase activity or its role in inhibiting transcription. ALP1 is the first example of a domesticated transposase acquiring a novel function as a PcG component. The antagonistic interaction of a modified transposase with the PcG machinery is novel and may have arisen as a means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity.

Abstract 1071: Age-dependent DNA methylation in normal breast epithelium and breast cancer

Abstract Breast cancer risk factors include age, genetic alterations, weight, diet and others. More recently accumulating evidence suggests that epigenetic alterations are frequent and play important role in breast cancer development and progression. Epigenetic alterations include changes in DNA methylation, histone modifications and miRNA expression in the absence of changes in DNA sequence. The epigenetic changes in cancer include global loss of DNA methylation that might lead to genomic instability and gain of methylation at many promoters of tumor suppressor genes that leads to gene silencing. Interestingly, work from our own laboratory and others have established that in many different tissues, DNA methylation changes due to age have similar patterns as to changes that occur in cancer. Therefore, the goal of this study is to identify and characterize age-dependent DNA methylation changes in normal breast epithelium and their contribution to breast cancer development. To differentiate between age-dependent and independent DNA methylation changes, we utilized DNA extracted from 27 primary human mammary epithelial cells (age range 33-82 years old) derived from adjacent or contralateral normal mammary tissue of breast cancer patients. We measured DNA methylation using a highly sensitive methodology developed in our laboratory called Digital Restriction Enzyme Analysis of Methylation (DREAM). We also studied DNA methylation in six different breast cancer cell lines by DREAM. We also used publically available 450K TCGA data for 685 breast tumor and 98 normal samples. Using bioinformatic approach, we have defined age dependent (Spearman R > |0.38|, p <0.05) and independent (Spearman R < |0.37|, p>0.05) sites that exhibit DNA methylation changes in normal breast epithelium. Interestingly, we found that the age-related genes are more seeded (exhibit low level of methylation) in their promoter CpG islands and are enriched for polycomb group target genes compared to the non-age related genes (p value = 0.032). Furthermore, these age-related genes (for example HOXD9, TDRD10, MYOD1, DPYS, GDA, GIPC2, FAM162B, LAMA1, PKDREJ, etc) have increased DNA methylation in tumors compared to the normal samples in TCGA with a methylation difference of up to 50%. These changes are significantly different compared to not-age related genes or random genes (p<0.0001). The age-related genes that gained DNA methylation in tumors in TCGA dataset, were also hypermethylated in breast cancer cell lines compared to immortalized human mammary epithelial cells. Thirty one percent of the common genes between TCGA data set and breast cancer cell lines, showed decreased mRNA expression in RNA-seq data available through the TCGA data portal. Therefore, in this study we have characterized age-dependent epigenetic changes in normal breast epithelium as potential breast cancer risk associated alterations. Citation Format: Shoghag B. Panjarian, Carolyn Slater, Jozef Madzo, Jaroslav Jelinek, Xiaowei Chen, Jean-Pierre Issa. Age-dependent DNA methylation in normal breast epithelium and breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1071. doi:10.1158/1538-7445.AM2015-1071

Abstract 3288: The KCNA5 promoter is hypermethylated in Ewing sarcoma and silencing contributes to cell proliferation

Abstract Potassium channels regulate a variety of biological processes and dysfunction of these channels contributes to cancer initiation and progression. We recently showed that the KCNA5-encoded channel, Kv1.5, is a target of polycomb-group (PcG)-dependent repression in aggressive pediatric solid tumors and that this epigenetic silencing of the Kv1.5 channel contributes to cell survival under hypoxic stress. In human cancer, the promoters of PcG target genes are often subject to aberrant DNA hypermethylation. Therefore, in the current study we investigated whether the KCNA5 locus is hypermethylated in Ewing sarcoma. The methylation status of KCNA5 was determined in tumor samples, non-transformed cells and a panel of cancer cell lines using a custom Illumina GoldenGate® methylation array and by MethyLight. Promoter methylation and expression of KCNA5 were measured by MethyLight and qRT-PCR, respectively, before and after exposure to decitabine. Proliferation was assessed in untreated and decitabine treated cells in the presence or absence of the Kv1.5 channel blocker diphenyl phosphine oxide-1 (DPO-1). Methylation array studies of normal tissues and Ewing sarcoma tumors and cell lines showed that the KCNA5 promoter is hypermethylated in Ewing sarcoma compared to normal tissues. This hypermethylation was confirmed by MethyLight analysis in an independent set of primary tumors and cell lines. These studies also showed that methylation was relatively higher in cell lines than primary tumors. Exposure of Ewing sarcoma cells to decitabine led to demethylation of the KCNA5 promoter and directly correlated with increased expression of the KCNA5 transcript. Decitabine treatment did not affect the viability of Ewing sarcoma cell lines; however it led to a decreased proliferation. Significantly, pharmacologic inhibition of the Kv1.5 channel by DPO-1 partially reversed the decitabine-induced reduction in cell proliferation in three different cell lines (TC-71, A673 and A4573). Together these studies show that the KCNA5 promoter is hypermethylated in Ewing sarcoma and that inactivation of the Kv1.5 channel promotes cell proliferation. This work identifies DNA methylation as another epigenetic mechanism that regulates KCNA5 expression in cancer and further implicates epigenetic repression of the Kv1.5 potassium ion channel in tumor pathogenesis. Citation Format: Katherine Ryland, Allegra Hawkins, Daniel J. Weisenberger, Scott Borinstein, Peter W. Laird, Jeffrey R. Martens, Elizabeth R. Lawlor. The KCNA5 promoter is hypermethylated in Ewing sarcoma and silencing contributes to cell proliferation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3288. doi:10.1158/1538-7445.AM2015-3288

Genome-wide activities of Polycomb complexes control pervasive transcription.

Polycomb group (PcG) complexes PRC1 and PRC2 are well known for silencing specific developmental genes. PRC2 is a methyltransferase targeting histone H3K27 and producing H3K27me3, essential for stable silencing. Less well known but quantitatively much more important is the genome-wide role of PRC2 that dimethylates ∼70% of total H3K27. We show that H3K27me2 occurs in inverse proportion to transcriptional activity in most non-PcG target genes and intergenic regions and is governed by opposing roaming activities of PRC2 and complexes containing the H3K27 demethylase UTX. Surprisingly, loss of H3K27me2 results in global transcriptional derepression proportionally greatest in silent or weakly transcribed intergenic and genic regions and accompanied by an increase of H3K27ac and H3K4me1. H3K27me2 therefore sets a threshold that prevents random, unscheduled transcription all over the genome and even limits the activity of highly transcribed genes. PRC1-type complexes also have global roles. Unexpectedly, we find a pervasive distribution of histone H2A ubiquitylated at lysine 118 (H2AK118ub) outside of canonical PcG target regions, dependent on the RING/Sce subunit of PRC1-type complexes. We show, however, that H2AK118ub does not mediate the global PRC2 activity or the global repression and is predominantly produced by a new complex involving L(3)73Ah, a homolog of mammalian PCGF3.

Polycomb-mediated silencing in neuroendocrine prostate cancer.

BackgroundNeuroendocrine prostate cancer (NEPC) is a highly aggressive subtype of prostate cancer (PCa) for which the median survival remains less than a year. Current treatments are only palliative in nature, and the lack of suitable pre-clinical models has hampered previous efforts to develop novel therapeutic strategies. Addressing this need, we have recently established the first in vivo model of complete neuroendocrine transdifferentiation using patient-derived xenografts. Few genetic differences were observed between parental PCa and relapsed NEPC, suggesting that NEPC likely results from alterations that are epigenetic in nature. Thus, we sought to identify targetable epigenetic regulators whose expression was elevated in NEPC using genome-wide profiling of patient-derived xenografts and clinical samples.ResultsOur data indicate that multiple members of the polycomb group (PcG) family of transcriptional repressors were selectively upregulated in NEPC. Notably, CBX2 and EZH2 were consistently the most highly overexpressed epigenetic regulators across multiple datasets from clinical and xenograft tumor tissues. Given the striking upregulation of PcG genes and other transcriptional repressors, we derived a 185-gene list termed ‘neuroendocrine-associated repression signature’ (NEARS) by overlapping transcripts downregulated across multiple in vivo NEPC models. In line with the striking upregulation of PcG family members, NEARS was preferentially enriched with PcG target genes, suggesting a driving role for PcG silencing in NEPC. Importantly, NEARS was significantly associated with high-grade tumors, metastatic progression, and poor outcome in multiple clinical datasets, consistent with extensive literature linking PcG genes and aggressive disease progression.ConclusionsWe have explored the epigenetic landscape of NEPC and provided evidence of increased PcG-mediated silencing associated with aberrant transcriptional regulation of key differentiation genes. Our results position CBX2 and EZH2 as potential therapeutic targets in NEPC, providing opportunities to explore novel strategies aimed at reversing epigenetic alterations driving this lethal disease.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-015-0074-4) contains supplementary material, which is available to authorized users.

Acceleration of age-associated methylation patterns in HIV-1-infected adults.

Patients with treated HIV-1-infection experience earlier occurrence of aging-associated diseases, raising speculation that HIV-1-infection, or antiretroviral treatment, may accelerate aging. We recently described an age-related co-methylation module comprised of hundreds of CpGs; however, it is unknown whether aging and HIV-1-infection exert negative health effects through similar, or disparate, mechanisms. We investigated whether HIV-1-infection would induce age-associated methylation changes. We evaluated DNA methylation levels at >450,000 CpG sites in peripheral blood mononuclear cells (PBMC) of young (20-35) and older (36-56) adults in two separate groups of participants. Each age group for each data set consisted of 12 HIV-1-infected and 12 age-matched HIV-1-uninfected samples for a total of 96 samples. The effects of age and HIV-1 infection on methylation at each CpG revealed a strong correlation of 0.49, p<1 x10-200 and 0.47, p<1x10-200. Weighted gene correlation network analysis (WGCNA) identified 17 co-methylation modules; module 3 (ME3) was significantly correlated with age (cor=0.70) and HIV-1 status (cor=0.31). Older HIV-1+ individuals had a greater number of hypermethylated CpGs across ME3 (p=0.015). In a multivariate model, ME3 was significantly associated with age and HIV status (Data set 1: βage= 0.007088, p=2.08 x 10-9; βHIV= 0.099574, p=0.0011; Data set 2: βage= 0.008762, p=1.27x 10-5; βHIV= 0.128649, p= 0.0001). Using this model, we estimate that HIV-1 infection accelerates age-related methylation by approximately 13.7 years in data set 1 and 14.7 years in data set 2. The genes related to CpGs in ME3 are enriched for polycomb group target genes known to be involved in cell renewal and aging. The overlap between ME3 and an aging methylation module found in solid tissues is also highly significant (Fisher-exact p=5.6 x 10-6, odds ratio=1.91). These data demonstrate that HIV-1 infection is associated with methylation patterns that are similar to age-associated patterns and suggest that general aging and HIV-1 related aging work through some common cellular and molecular mechanisms. These results are an important first step for finding potential therapeutic targets and novel clinical approaches to mitigate the detrimental effects of both HIV-1-infection and aging.

Genomic, Epigenomic, and Transcriptomic Profiling towards Identifying Omics Features and Specific Biomarkers That Distinguish Uterine Leiomyosarcoma and Leiomyoma at Molecular Levels.

Uterine leiomyosarcoma (LMS) is the worst malignancy among the gynecologic cancers. Uterine leiomyoma (LM), a benign tumor of myometrial origin, is the most common among women of childbearing age. Because of their similar symptoms, it is difficult to preoperatively distinguish the two conditions only by ultrasound and pelvic MRI. While histopathological diagnosis is currently the main approach used to distinguish them postoperatively, unusual histologic variants of LM tend to be misdiagnosed as LMS. Therefore, development of molecular diagnosis as an alternative or confirmatory means will help to diagnose LMS more accurately. We adopted omics-based technologies to identify genome-wide features to distinguish LMS from LM and revealed that copy number, gene expression, and DNA methylation profiles successfully distinguished these tumors. LMS was found to possess features typically observed in malignant solid tumors, such as extensive chromosomal abnormalities, overexpression of cell cycle-related genes, hypomethylation spreading through large genomic regions, and frequent hypermethylation at the polycomb group target genes and protocadherin genes. We also identified candidate expression and DNA methylation markers, which will facilitate establishing postoperative molecular diagnostic tests based on conventional quantitative assays. Our results demonstrate the feasibility of establishing such tests and the possibility of developing preoperative and noninvasive methods.

The Biological Function of DNA Hypermethylation in Murine MDS Model Lacking Tet2 and Ezh2

Mutations of epigenetic regulators are often found in patients with myelodysplastic syndrome (MDS). Furthermore, DNA methylation inhibitors have a therapeutic impact on MDS. However, it remains unknown how altered DNA methylation promotes the development of MDS. We have shown that concurrent depletion of Tet2 and Ezh2 in hematopoietic cells significantly promotes the development of MDS in vivo by utilizing hypomorphic Tet2 (Tet2KD/KD) mice and Ezh2 conditional knockout mice (Cre-ERT;Ezh2fl/fl)(Muto T, et al. J Exp Med 2014).In order to determine how DNA methylation contributes to the formation of MDS in Tet2KD/KDEzh2Δ/Δ mice, we transplanted wild type (WT), Tet2KD/KD, Cre-ERT;Ezh2fl/fl, and Cre-ERT;Tet2KD/KDEzh2fl/fl fetal liver cells in lethally irradiated CD45.1+ recipient mice, and deleted Ezh2 at 4 weeks post-transplantation. We then performed reduced representation bisulfite sequence (RRBS) in Lin-Sca1+Kit+ (LSK) cells isolated from Tet2KD/KD and Ezh2Δ/Δ mice at 3 and 7 months post-deletion and WT and Tet2KD/KDEzh2Δ/Δ mice at 5 months post-deletion. We defined ≥10% difference of methylation in test cells compared with that in WT cells as hyper- or hypo-differentially methylated regions (DMRs) (p-value<0.01). We found that Ezh2Δ/Δ LSK cells gain significantly larger number of hyper-DMRs at CpG islands (CGIs) over time compared with Tet2KD/KD LSK cells. At 8 months post-deletion, Tet2KD/KD and Ezh2Δ/Δ LSK cells gained hyper-DMRs in 196 and 366 out of 12677 promoters, and 106 and 306 out of 11504 CGIs, respectively. Tet2KD/KDEzh2Δ/Δ-MDS LSK cells at 5 months post-deletion had hyper- and hypo-DMRs in 109 and 51 out of 12677 promoters, and 124 and 27 out of 11504 CGIs, respectively. Hyper-CGI DMRs of Tet2KD/KDEzh2Δ/Δ-MDS LSK cells largely overlapped with those of Tet2KD/KD and Ezh2Δ/Δ LSK cells (p<1.00E-16). Nonetheless, a significant number of hyper-CGI DMRs were newly generated in Tet2KD/KDEzh2Δ/Δ-MDS LSK cells, suggesting unique impact of combined loss of Tet2 and Ezh2 on epigenome. Of note, hyper-DMRs in this mouse MDS model significantly overlapped with those in human CD34+ cells of MDS patients (Maegawa S, et al. Genome Research 2014) (40 genes, p=0.0001). As reported in solid tumor and aging stem cells, polycomb-group (PcG) protein targets were significantly enriched among hyper-CGI DMRs in LSK cells of all three genotypes; Tet2KD/KD, Ezh2Δ/Δ, and Tet2KD/KDEzh2Δ/Δ-MDS LSK cells. Indeed, hypermethylated CGIs were enriched for genes encoding DNA binding transcription factors (p=8.96E-05) and cell differentiation (p=3.98E-05) in GO analysis, suggesting that DNA methylation involves the PcG targets such as developmental regulator genes that regulate hematopoietic cell differentiation in the pathogenesis of MDS.To determine an association between levels of differential DNA methylation and transcription of genes, we next performed DNA microarray analysis by using LSK cells. As several studies reported, we observed no significant association between levels of DNA methylation and gene expression (R2=0.003). However, 27 hypermethylated genes showed reduced levels of gene expression in Tet2KD/KDEzh2Δ/Δ-MDS LSK cells. Those included key transcription factors and epigenetic modifiers for hematopoiesis, such as Gata2, Gata3, Evi1, and Bcor.Finally, we examined whether decitabine, a demethylating agent, reverses the DNA hypermethylation of Tet2KD/KDEzh2Δ/Δ-MDS LSK cells in vivo. Although the administration of decitabine into secondary recipients of MDS BM cells did not improve the survival of mice, platelet counts were significantly increased in decitabine-treated MDS mice, compared to the control MDS mice. After 4 weeks of treatment, a partial restoration of DNA hypermethylation was observed in the decitabine-treated MDS mice (34 out of 124 CGIs; p<1.00-16E). These regions were again enriched in DNA binding transcription factors (p=1.72E-05) and cell differentiation (p=2.25E-07) in GO analysis.Taken together, our work unveiled the biological function of DNA hypermethylation in the pathogenesis of MDS, and will give a clue to understanding how demethylating agents improve the outcome of patients with MDS. DisclosuresNo relevant conflicts of interest to declare.