methyl-DNA Binding Proteins Research Articles

Epigenetic gene regulation in plants and its potential applications in crop improvement.

DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in plant growth, development and adaptation. The cellular DNA methylation level is tightly regulated by the combined action of DNA methyltransferases and demethylases. Protein complexes involved in the targeting and interpretation of DNA methylation have been identified, revealing intriguing roles of methyl-DNA binding proteins and molecular chaperones. Structural studies and in vitro reconstituted enzymatic systems have provided mechanistic insights into RNA-directed DNA methylation, the main pathway catalysing de novo methylation in plants. A better understanding of the regulatory mechanisms will enable locus-specific manipulation of the DNA methylation status. CRISPR-dCas9-based epigenome editing tools are being developed for this goal. Given that DNA methylation patterns can be stably transmitted through meiosis, and that large phenotypic variations can be contributed by epimutations, epigenome editing holds great promise in crop breeding by creating additional phenotypic variability on the same genetic material.

INTELLECTUAL DISABILITY CLASSIFICATION, CAUSES, EPIGENETIC MECHANISMS AND TREATMENT

Intellectual disability (ID) is a condition characterized by defective adaptive and cognitive attitude that can occur with various mental disorders, such as attention deficit/hyperactivity and autism spectrum disorder. It may also be associated with malformation syndromes affecting other organs. Genetic studies have linked several chromatin-modifying enzymes and epigenetic regulators to ID disorders (IDDs). This review explores how dysfunction in histone modifiers, chromatin remodelers, and methyl-DNA binding proteins can cause neurodevelopmental deformities and alter brain plasticity. The use of mouse models generated through human genetics has allowed researchers to uncover the molecular basis of ID and explore potential therapeutic strategies. Understanding the chromatin regulators associated with IDDs has broader implications for treating other IDDs, as they target common downstream genes and cellular functions. Investigating these disorders can also shed light on the function of chromatin regulators in brain growth, plasticity, and gene regulation, leading to new insights into fundamental questions in neurobiology.

Single-molecule dissection of the interaction between a methyl-DNA binding protein and chromatin.

The methyl-CpG binding protein 2 (MeCP2) is a prominent DNA methylation reader that is essential for proper gene expression programming and normal functioning of nerve cells. Mutations in MeCP2 cause Rett syndrome, a severe neurological disorder mainly affecting females and characterized by psychiatric and motor regression at 6-18 months. Despite decades of efforts, there are currently no approved therapies that directly target MeCP2 loss of function. One primary reason for the lack of MeCP2-targeted interventions is an inadequate understanding of how MeCP2 reads methylated DNA within eukaryotic chromatin. To address this knowledge gap, we developed an experimental platform that combines optical tweezers and single-molecule fluorescence microscopy to directly visualize the dynamic behavior of MeCP2 on chromatin. This assay enabled us to discover unexpectedly that nucleosomes serve as higher affinity substrates for MeCP2 than CpG methylated DNA, challenging the canonical view of MeCP2 as purely a methyl-CpG DNA reader. Instead, MeCP2 recognizes methylated DNA sites only after exhausting all available nucleosome sites. We further showed the high-affinity MeCP2-nucleosome interaction is dependent on MeCP2's disordered C-terminal domain. In addition, we demonstrated counterintuitively that MeCP2 and linker histone H1—two highly abundant nuclear proteins—can occupy the same nucleosome sites. Taken together, our results indicate that nucleosomes heavily regulate the availability and function of MeCP2 in the nucleus. Moreover, this work paves the way for mechanistic interrogation of Rett syndrome mutations and their impact on MeCP2 function at chromatin.

Plasma EBV DNA Methylation: Evidence of EBV Lytic Infection in HIV(+) EBV(+) Plasmablastic Lymphoma

Background: Among people living with HIV, plasmablastic lymphoma (PBL) and classical Hodgkin lymphoma (HL) are almost uniformly associated with Epstein-Barr virus (EBV). Immunohistochemical studies have demonstrated high levels of lytic gene expression in PL,1 whereas EBV(+) HL shows exclusively latent viral gene expression. EBV virion DNA is never CpG methylated, but tumor-derived plasma EBV is CpG methylated as previously shown by our group in EBV(+) HL and nasopharyngeal carcinoma (NPC).2 Others have also presented evidence that patterns of CpG methylation of plasma EBV DNA varies between people with NPC and non-malignant EBV(+) conditions.3 To better characterize the nature of plasma EBV in patients with lymphoma, we investigated EBV DNA copy number and EBV DNA methylation in HIV-associated PBL and HL. Methods: With appropriate approvals from the Human Research Ethics Committee of the University of the Witwatersrand and the Johns Hopkins Institutional Review Boards, we collected plasma from newly diagnosed untreated patients with HIV and PBL or HL in Johannesburg, South Africa. Diagnostic biopsy specimens were reviewed in Baltimore by a hematopathologist to confirm the diagnosis and Epstein-Barr encoding region (EBER) in situ hybridization was performed to determine EBV association. Plasma EBV copies were measured by standard qPCR targeting the BamW repeats. qPCR using the same primers was also performed after capture with methyl-DNA binding protein 2 (MBD2) magnetic beads, where the captured fraction represents methylated DNA and the flow-through represents unmethylated DNA. Results: We studied plasma from 7 patients with PBL and 12 patients with HL. Four of five PBL tumors were EBV (+) and eight of 10 HL tumors were EBV (+) by tissue EBER in situ hybridization. Analysis of plasma EBV DNA copy number showed overlapping levels of EBV DNA (median 2.7 Log10 copy/mL in PBL and 3.2 Log10 copy/mL in HL) (Fig. 1). Patients with at least 1.5 Log10 copy/mL of EBV underwent CpG methylation evaluation, which showed very different EBV CpG methylation indices. The EBV methylation index was highly variable in PBL (median of 51%) and was uniformly high in HL (median of 97%). Conclusions: Although plasma from plasmablastic lymphoma patients show high EBV copy number, the characteristic of that EBV DNA is very different from the plasma EBV detected in Hodgkin lymphoma patients. This difference is hypothesized to be related to evidence of viral lytic gene expression seen in PBL. The degree of plasma EBV DNA methylation may have broad implications for lymphoma diagnosis and subtyping.

TRIM28 regulates transcriptional activity of methyl-DNA binding protein Kaiso by SUMOylation

Kaiso is a methyl DNA binding transcriptional factor involved in cell cycle control, WNT signaling, colon inflammation, and cancer progression. Recently, it was shown that SUMOylation dynamically modulates the transcriptional activity of Kaiso. However, factors involved in SUMOylation of Kaiso are unknown. Here we show that TRIM28 enhances SUMOylation of Kaiso leading to a decreased methyl-dependent repression ability. TRIM28 is a scaffold protein that regulates transcription and posttranslational modifications of factors involved in cell cycle progression, DNA damage, and viral gene expression. It has SUMO and ubiquitin E3 ligase activity. Here, we defined the domains involved in Kaiso-TRIM28 interaction. The RBCC domain of TRIM28 interacts with the BTB/POZ domain and the zinc fingers of Kaiso. The PHD-bromodomain of TRIM28 is sufficient for the interaction with zinc fingers of Kaiso. Additionally, we found that Kaiso enhances SUMOylation of TRIM28. Altogether our data suggest self-enhancement of SUMOylation of both Kaiso and TRIM28 that affects transcriptional activity of Kaiso.

Genetic analysis implicates a molecular chaperone complex in regulating epigenetic silencing of methylated genomic regions

DNA cytosine methylation confers stable epigenetic silencing in plants and many animals. However, the mechanisms underlying DNA methylation-mediated genomic silencing are not fully understood. We conducted a forward genetic screen for cellular factors required for the silencing of a heavily methylated p35S:NPTII transgene in the Arabidopsis thaliana rdm1-1 mutant background, which led to the identification of a Hsp20 family protein, RDS1 (rdm1-1 suppressor 1). Loss-of-function mutations in RDS1 released the silencing of the p35S::NPTII transgene in rdm1-1 mutant plants, without changing the DNA methylation state of the transgene. Protein interaction analyses suggest that RDS1 exists in a protein complex consisting of the methyl-DNA binding domain proteins MBD5 and MBD6, two other Hsp20 family proteins, RDS2 and IDM3, a Hsp40/DNAJ family protein, and a Hsp70 family protein. Like rds1 mutations, mutations in RDS2, MBD5, or MBD6 release the silencing of the transgene in the rdm1 mutant background. Our results suggest that Hsp20, Hsp40, and Hsp70 proteins may form a complex that is recruited to some genomic regions with DNA methylation by methyl-DNA binding proteins to regulate the state of silencing of these regions.

Kaiso Regulates DNA Methylation Homeostasis.

Gain and loss of DNA methylation in cells is a dynamic process that tends to achieve an equilibrium. Many factors are involved in maintaining the balance between DNA methylation and demethylation. Previously, it was shown that methyl-DNA protein Kaiso may attract NCoR, SMRT repressive complexes affecting histone modifications. On the other hand, the deficiency of Kaiso resulted in reduced methylation of ICR in H19/Igf2 locus and Oct4 promoter in mouse embryonic fibroblasts. However, nothing is known about how Kaiso influences DNA methylation at the genome level. Here we show that deficiency of Kaiso led to whole-genome hypermethylation, using Kaiso deficient human renal cancer cell line obtained via CRISPR/CAS9 genome editing. However, Kaiso serves to protect genic regions, enhancers, and regions with a low level of histone modifications from demethylation. We detected hypomethylation of binding sites for Oct4 and Nanog in Kaiso deficient cells. Kaiso immunoprecipitated with de novo DNA methyltransferases DNMT3a/3b, but not with maintenance methyltransferase DNMT1. Thus, Kaiso may attract methyltransferases to surrounding regions and modulate genome methylation in renal cancer cells apart from being methyl DNA binding protein.

FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin.

Association of RNA polymerase V (Pol V) with chromatin is a critical step for RNA- directed DNA methylation (RdDM) in plants. Although the methylated DNA-binding proteins SUVH2 and SUVH9 and the chromatin remodeler-containing complex DRD1-DMS3-RDM1 are known to be required for the association of Pol V with chromatin, the molecular mechanisms underlying the association of Pol V with different chromatin environments remain largely unknown. Here we found that SUVH9 interacts with FVE, a homolog of the mammalian retinoblastoma-associated protein, which has been previously identified as a shared subunit of the histone deacetylase complex and the polycomb-type histone H3K27 trimethyltransferase complex. We demonstrated that FVE facilitates the association of Pol V with chromatin and thus contributes to DNA methylation at a substantial subset of RdDM target loci. Compared with FVE-independent RdDM target loci, FVE-dependent RdDM target loci are more abundant in gene-rich chromosome arms than in pericentromeric heterochromatin regions. This study contributes to our understanding of how the association of Pol V with chromatin is regulated in different chromatin environments.

A novel protein complex that regulates active DNA demethylation in Arabidopsis.

Active DNA demethylation is critical for altering DNA methylation patterns and regulating gene expression. The 5-methylcytosine DNA glycosylase/lyase ROS1 initiates a base-excision repair pathway for active DNA demethylation and is required for the prevention of DNA hypermethylation at 1 000s of genomic regions in Arabidopsis. How ROS1 is regulated and targeted to specific genomic regions is not well understood. Here, we report the discovery of an Arabidopsis protein complex that contains ROS1, regulates ROS1 gene expression, and likely targets the ROS1 protein to specific genomic regions. ROS1 physically interacts with a WD40 domain protein (RWD40), which in turn interacts with a methyl-DNA binding protein (RMB1) as well as with a zinc finger and homeobox domain protein (RHD1). RMB1 binds to DNA that is methylated in any sequence context, and this binding is necessary for its function in vivo. Loss-of-function mutations in RWD40, RMB1, or RHD1 cause DNA hypermethylation at several tested genomic regions independently of the known ROS1 regulator IDM1. Because the hypermethylated genomic regions include the DNA methylation monitoring sequence in the ROS1 promoter, plants mutated in RWD40, RMB1, or RHD1 show increased ROS1 expression. Importantly, ROS1 binding to the ROS1 promoter requires RWD40, RMB1, and RHD1, suggesting that this complex dictates ROS1 targeting to this locus. Our results demonstrate that ROS1 forms a protein complex with RWD40, RMB1, and RHD1, and that this novel complex regulates active DNA demethylation at several endogenous loci in Arabidopsis.

Application of affinity capillary electrophoresis in the study of protein-DNA interactions

Protein-DNA interactions play essential roles in various biological events that determine the cell fate. Research on the molecular mechanism of protein-DNA interactions has helped elucidate diverse fundamental life processes, thereby providing theoretical guidance for establishing clinical treatment and screening potential drug of target diseases. Furthermore, well-known protein-DNA interactions have been utilized to develop advanced bioengineering and bioanalytical techniques, therefore providing robust technical support for related research. Hence, it is important to establish sensitive and rapid analytical methods to study protein-DNA interactions. High-performance capillary electrophoresis (CE) has been widely used in many research fields such as chemistry, life sciences, and environmental sciences, mainly due to its advantages including ultra-high separation efficiency, extremely low sample consumption, and short analysis time. For instance, affinity capillary electrophoresis (ACE) has become an important analytical tool for investigating molecular interactions. In this paper, we review the applications of ACE in studying protein-DNA interactions since it was first proposed in 1992, addressing previous significant work in this field. Three major aspects have been summarized in this review: (1) brief introduction to the development of ACE technique; (2) applications of ACE in the fundamental research on the molecular mechanism of protein-DNA interactions; and (3) applications of well-known protein-DNA interactions in CE-based detection of target molecules and reactions. In the first aspect, along with the concept and separation modes of ACE, general strategies to enhance the analytical ability of ACE are briefly introduced. In the second aspect, the applications of ACE in studying several important protein-DNA interactions involving transcription factors (e.g., GCN4), DNA repair proteins (e.g., UvrA, UvrB, and RecA), and methylated DNA-binding proteins (MBDs) are reviewed. In the third aspect, the applications of well-known molecular interactions (e.g., antigen-antibody, aptamer-target, etc.) to facilitate CE-based detection of target molecules (e.g., DNA adducts, DNA methylation, microRNA, single nucleotide polymorphism, etc.) and target reactions (e.g., DNA strand exchange) are addressed. Finally, we prospect and discuss the advancements of ACE that can be established in future studies. The following two aspects should be improved in future ACE analysis: (1) the advantages of extremely low volume consumption and short analysis time should be fully utilized to develop sensitive and high-throughput CE platforms for the assessment of rare biological samples and massive uncertain samples, respectively; (2) ACE should be combined with other advanced techniques, such as DNA sequencing and mass spectrometry, to rapidly screen and identify the precise interacting sites of unknown protein-DNA interactions.

Resveratrol up-regulates ATP2A3 gene expression in breast cancer cell lines through epigenetic mechanisms.

Resveratrol (RSV) is a phytoestrogen which has been related to chemoprevention of several types of cancer. In this work, we show up to a 6-fold increased expression of ATP2A3 gene induced by RSV that triggers apoptosis and changes of intracellular Ca2+ management in MCF-7 and MDA-MB-231 breast cancer cell lines. We explored epigenetic mechanisms for that RSV-induced ATP2A3 up-regulation. The results indicate that RSV-induced ATP2A3 up-regulation correlates with about 50% of reduced HDAC activity and reduced nuclear HDAC2 expression and occupancy on ATP2A3 promoter, increasing the global acetylation of histone H3 and the enrichment of histone mark H3K27Ac on the proximal promoter of the ATP2A3 gene in MDA-MB-231 cells. We also quantified HAT activity, finding that it can be boosted with RSV treatment; however, pharmacological inhibition of p300, one of the main HATs, did not have significant effects in RSV-mediated ATP2A3 gene expression. Additionally, DNMT activity was also reduced in cells treated with RSV, as well as the expression of Methyl-DNA binding proteins MeCP2 and MBD2. However, analysis of the methylation pattern of ATP2A3 gene promoter showed un-methylated promoter in both cell lines. Taken together, the results of this work help to explain, at the molecular level, how ATP2A3 gene is regulated in breast cancer cells, and the benefits of RSV intake observed in epidemiological data, studies with animals, and in vitro models.

Abstract 5881: Novel inhibitors of the epigenetic reader protein MBD2

Abstract DNA hypermethylation can trigger silencing of tumor suppressor genes during cancer development and progression, partly through binding by methylated-DNA binding proteins (MBD), such as MBD2, that function as “epigenetic readers” and recruit co-repressor complexes to promote gene repression. Inhibiting MBD2-mediated repression represents an attractive cancer therapeutic strategy. Here, we used a cell-based screen to identify small molecules capable of reactivating hypermethylated promoter sequences. We used biochemical, molecular biologic, and pharmacologic approaches to characterize mechanism of action of identified MBD2 inhibitors. A subset of these compounds represent a new class of inhibitors capable of selectively antagonizing interactions between MBD2 and methylated DNA, leading to reactivation of the hypermethylated gene GSTP1 and the epigenetically silenced retinoic acid signaling pathway. Combinations of one of the newly identified MBD2 inhibitors, KCC-08, with the retinoic acid receptor agonist, isotretinoin, significantly reduced cancer cell growth/survival in vitro and in vivo. These novel MBD2 inhibitors are thus positioned for further pharmacologic lead development for use as probes to interrogate epigenetic gene silencing mechanisms and as cancer therapeutics. Citation Format: Hugh Giovinazzo, Zachary R. Reichert, Andries Bergman, Xiaohui Lin, Nicolas Wyhs, David Esopi, Ajay Vaghasia, Jianyong Liu, Yash Jain, Akshay Bhamidipati, Ruchama Steinberg, Traci Speed, Matthew Vaughn, Yonggang Zhang, Nate Brennen, Theodore Deweese, Srinivasan Yegnasubramanian, William G. Nelson. Novel inhibitors of the epigenetic reader protein MBD2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5881.

Epigenetic Etiology of Intellectual Disability.

Intellectual disability (ID) is a prevailing neurodevelopmental condition associated with impaired cognitive and adaptive behaviors. Many chromatin-modifying enzymes and other epigenetic regulators have been genetically associated with ID disorders (IDDs). Here we review how alterations in the function of histone modifiers, chromatin remodelers, and methyl-DNA binding proteins contribute to neurodevelopmental defects and altered brain plasticity. We also discuss how progress in human genetics has led to the generation of mouse models that unveil the molecular etiology of ID, and outline the direction in which this field is moving to identify therapeutic strategies for IDDs. Importantly, because the chromatin regulators linked to IDDs often target common downstream genes and cellular processes, the impact of research in individual syndromes goes well beyond each syndrome and can also contribute to the understanding and therapy of other IDDs. Furthermore, the investigation of these disorders helps us to understand the role of chromatin regulators in brain development, plasticity, and gene expression, thereby answering fundamental questions in neurobiology.

Neonatal Exposure to 6-n-Propyl-Thiouracil, an Anti-Thyroid Drug, Alters Expression of Hepatic DNA Methyltransferases, Methyl CpG-Binding Proteins, Gadd45a, p53, and PCNA in Adult Male Rats

Background: Neonatal 6-n-propyl-2-thiouracil (PTU) exposure to male rats is reported to impair liver function in adulthood. However, the mechanism by which the drug impairs liver function is not well known. Objectives: The objectives of the study were to investigate the effects of neonatal exposure of PTU on the expression of DNA methyltransferases (DNMTs), methyl-DNA binding proteins (MBDs), Gadd45a, p53, and proliferating cell nuclear antigen (PCNA) in adult rat liver. Methods: The effects of neonatal transient (from birth to 30 days of age) and persistent (from birth to 90 days of age) treatment of PTU on DNA damage and on the expression of p53, PCNA, DNMTs, and MBDs were investigated at transcriptional and translational levels in male adult liver. Results: Persistent exposure to PTU from birth caused significant downregulation of expression of DNMT1 and DNMT3a and upregulation of DNMT3b, MBD4, and Gadd45a without any damage to DNA. Although MeCp2 transcripts were significantly low in the liver of adult rats after persistent exposure to PTU compared to controls, its translated products were significantly higher than in controls. The expression of p53 and PCNA in PTU-treated rats was significantly higher and lower, respectively, than that in control rats. Conclusion: The results suggest that neonatal exposure of male rats to PTU resulted in alteration in the expression of proteins that are associated with DNA methylation and genome stabilization in adult rat liver.

Regulation and function of MeCP2 Ser421 phosphorylation in U50488-induced conditioned place aversion in mice.

Phosphorylation of the methyl DNA-binding protein MeCP2 at Ser421 (pMeCP2-S421) is induced in corticolimbic brain regions during exposure to drugs of abuse and modulates reward-driven behaviors. However, whether pMeCP2-S421 is also involved in behavioral adaptations to aversive drugs is unknown. Our goal was to establish the role and regulationof pMeCP2-S421 in corticolimbic brain regions of mice upon acute treatment with the kappa opioid receptor agonist U50488 and during the expression of U50488-induced conditioned place aversion (CPA). pMeCP2-S421 levels were measured in the nucleus accumbens (NAc), prelimbic cortex, infralimbic cortex (ILC), and basolateral amygdala (BLA) of male mice after intraperitoneal administration of U50488 and upon the expression of U50488-induced CPA. Fos was measured as marker of neural activity in the same brain regions. U50488-induced CPA and Fos levels were compared between knockin (KI) mice that lack pMeCP2-S421 and their wild-type (WT) littermates. U50488 administration acutely induced pMeCP2-S421 and Fos selectively in the NAc but did not alter MeCP2 levels in any brain region. U50488-induced CPA was associated with decreased pMeCP2-S421 in the ILC and BLA and induced Fos in the BLA. MeCP2 KI mice showed CPA indistinguishable from their WT littermates, but they also showed less BLA Fos induction upon CPA. These data are the first to show that pMeCP2-S421 is induced in the brain acutely after U50488 administration but not upon U50488-induced CPA. Although pMeCP2-S421 is not required for U50488-induced CPA, this phosphorylation event may contribute to molecular plasticities in brain regions that govern aversive behaviors.

Abstract 5035: MDB-seq screening of muscle-invasive urothelial carcinoma revealed unpredicted novel tumor suppressor genes

Abstract Bladder cancer (BC) is among the most frequent cancers in the United States. More than 70% patients suffer from superficial disease called non-muscle invasive bladder cancer (NMIBC) which, after the first successful surgery, has favorable survival but high risk of recurrence; on the other hand, muscle-invasive urothelial carcinoma (MIBC) is less prevalent but typically associated with a relatively poor prognosis. Since BC has been largely described as a multifactorial disease, with some DNA mutational component and strong evidence supporting an important role performed by the exposure to environmental factors, mainly derived from tobacco smoking and occupational hazards, consequent epigenetic DNA alterations could play important pathological role and also be used as markers for detection and stratification of the disease. In order to discover new methylated genes we performed novel sequential high throughput Methyl-DNA Binding (MDB) proteins Pull-down followed by large genome sequencing of 5 primary MIBC (not subject to previous therapy nor BCG) versus their normal counterparts. After Bioinformatic cross-analysis between the enriched sequences in our MDBseq experiment (corresponfing to 85 genes) and publicly available database (BC TCGA), we have come up to a list containing 16 hypermethylated genes in BC (our «consensus genes»). From the first unbiased analysis of this list, we have found some genes already found as important and/or hypermethylated in BC (as for example, CDKN2A, Sall3, Nkx6-2, CDO1), confirming the validity of our approach. Interestingly, we have observed high presence of transcription factors (homeobox, Paired, Zn fingers) and proteins involved in fundamental developmental processes. Among the newly hypermethylated genes in BC, we have chosen VIPR2 for further characterization. VIPR2 encodes the vasoactive intestinal peptide receptor VPAC2, a G-protein-coupled receptor that is expressed in a variety of tissues (expressed throughout the central nervous system and the periphery); it binds VIP14, activates cyclic AMP (cAMP)-signaling and PKA. The VIP-VPAC2 signaling pathway has been implicated in several neural and behavioral processes and is known to influence circadian rhythms and cognition. We first confirmed inverse correlation between diminished expression and promoter methylation in 11 BC cell lines (5637, HT-1376, J82, SW780, UM-UC-3, BFTC-905, BFTC-909, Scaber, RT4, T24) and a normal human urinary tract epithelium immortalized cell line SV-HUC-1 (HUC-1). Next, we determined that pharmacological unmasking with DNA methylation transferases (DNMTs) inhibitors (5-Aza-deoxycytidine) re-expressed the transcript in the cells analyzed. We are in the process of analyzing VIPR2 expression and promoter methylation in primary BC samples. After confirming in primary BC samples, we will further characterize the role of VIPR2 in bladder cancer pathogenesis. Citation Format: Elisa Guida, Luigi Marchionni, Rachel Goldberg, Mark Schoenberg, Trinity Bivalaqua, George J. Netto, Mohammad O. Moque, David Sidransky. MDB-seq screening of muscle-invasive urothelial carcinoma revealed unpredicted novel tumor suppressor genes. [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 5035.

Behavioral phenotyping of Kaiso-deficient mice

Kaiso is a methyl DNA-binding protein, which participates in the epigenetic regulation of gene expression. It binds methylated DNA with its zinc-finger domain and recruits repressive protein complexes to the methylated DNA fragments by the interaction of the BTB/POZ domain with the complex of NCoR corepressor and histone deacetylase, thereby performing transcription repression. A Kaiso-deficient mouse strain (KO) with the C57BL/6 strain background has been bred. Here we compare the behavior of KO mice and wild-type control C57BL/6 mice (WT) in the classic battery of behavioral tests, including the open field, elevated plus maze, and forced swim tests. We have shown that knockout of the Kaiso gene increases the locomotory and exploratory activities of KO mice in the open field test. Kaiso-deficient mice spend more time in the center of the open field than WT mice. No effect of Kaiso gene knockout on anxietyrelated behavior has been observed in the elevated plus-maze. However, Kaiso gene deficiency produces a pronounced antidepressant-like effect in the forced swim test: Unlike WT mice, KO mice do not show any depressive-like freezing in this test. These results are the first piece of experimental evidence for the involvement of Kaiso protein in the regulation of brain functioning and beha­vior. The Kaiso-deficient strain is a new and promising model of the genetic, molecular, and neuronal mechanisms mediating the epigenetic regulation of brain functions and behavior.

EPIG-01THE FUNCTION OF CHROMATIN-MODIFYING ENZYMES IN GBM CELL APOPTOSIS

Emerging evidence suggests that apoptotic resistance in cancers is associated with aberrant expression of the key components of the apoptotic program. However, how these components are regulated at an epigenetic level is not understood. In this study, we aimed to identify novel epigenetic mechanisms regulating the response of Glioblastoma Multiforme (GBM) cells to a pro-apoptotic ligand and an emerging therapeutic candidate, TRAIL. To this end, we conducted a short-hairpin RNA (shRNA) screen to assess the function of chromatin modifying-enzymes in TRAIL-induced apoptosis. We employed 2-3 shRNAs/gene to interrogate the role of 47 genes in DNA and histone modification pathways. Accordingly, we tested shRNAs targeting DNA-methyltransferases (DNMTs), Histone-Methyltransferases (HMTs), Histone demethylases (HDMs), Methyl-DNA binding proteins, and Polycomb complex members (PrC). Upon infection with individual shRNAs, U87MG cells were tested for their TRAIL response using cell viability assays. As a result, we identified KDM2B, an H3K36-specific HDM, as a novel regulator of TRAIL response. Accordingly, silencing of KDM2B significantly enhanced TRAIL sensitivity and accelerated the apoptosis process, as revealed by live cell imaging experiments. In order to decipher the downstream molecular pathways regulated by KDM2B, we examined expression levels of apoptosis-related genes by RNA-sequencing and quantitative PCR, and observed de-repression of pro-apoptotic genes and repression of anti-apoptotic genes upon KDM2B silencing. We also observed attenuated tumor growth upon KDM2B silencing in vivo. Taken together, our findings suggest a novel mechanism where the key apoptosis components are under epigenetic control of KDM2B in GBM cells. Therefore, identifying the direct targets of KDM2B might provide a new understanding of apoptosis response in GBMs and aid in the design of successful pro-apoptotic therapies.

Epigenetic regulation of liver fibrosis

Fibrosis is a common and important pathology associated with progressive chronic liver diseases and underlies the development of cirrhosis and hepatocellular carcinoma. Research into the molecular regulation of fibrosis has discovered that it is under the control of a number of epigenetic mechanisms including DNA methylation, histone modifications and the activities of non-coding RNAs. A deeper understanding of how epigenetic regulators such as DNA methyltranserases, methyl-DNA binding proteins, histone modifying enzymes and regulatory RNA molecules impact on the fibrogenic process is expected to result in new biomarkers for disease progression as well as novel therapeutic targets. The aim of this mini-review is to briefly introduce the reader to the major epigenetic regulators so far identified as being implicated in fibrosis.

The tumour suppressor CHD5 forms a NuRD-type chromatin remodelling complex.

Eukaryotic gene expression is developmentally regulated, in part by chromatin remodelling, and its dysregulation has been linked to cancer. CHD5 (chromodomain helicase DNA-binding protein 5) is a tumour suppressor gene (TSG) that maps to a region of consistent deletion on 1p36.31in neuroblastomas (NBs) and other tumour types. CHD5 encodes a protein with chromatin remodelling, helicase and DNA-binding motifs that is preferentially expressed in neural and testicular tissues. CHD5 is highly homologous to CHD3 and CHD4, which are the core subunits of nucleosome remodelling and deacetylation (NuRD) complexes. To determine if CHD5 forms a similar complex, we performed studies on nuclear extracts from NBLS, SY5Y (both with endogenous CHD5 expression), NLF (CHD5 null) and NLF cells stably transfected with CHD5 cDNA (wild-type and V5-histidine-tagged). Immunoprecipitation (IP) was performed with either CHD5 antibody or antibody to V5/histidine-tagged protein. We identified NuRD components both by GST-FOG1 (Friend Of GATA1) pull-down and by IP. We also performed MS/MS analysis to confirm the presence of CHD5 or other protein components of the NuRD complex, as well as to identify other novel proteins. CHD5 was clearly associated with all canonical NuRD components, including metastasis-associated protein (MTA)1/2, GATA zinc finger domain containing 2A (GATAD2A), histone deacetylase (HDAC)1/2, retinoblastoma-binding protein (RBBP)4/7 and methyl DNA-binding domain protein (MBD)2/3, as determined by Western blotting and MS/MS. Our data suggest CHD5 forms a NuRD complex similar to CHD4. However, CHD5-NuRD may also have unique protein associations that confer functional specificity and may contribute to normal development and to tumour suppression in NB and other cancers.