Epigenetic Properties Research Articles

Novel curcumin analog C66 prevents diabetic nephropathy via JNK pathway with the involvement of p300/CBP-mediated histone acetylation

Glomerulosclerosis and interstitial fibrosis represent the key events in development of diabetic nephropathy (DN), with connective tissue growth factor (CTGF), plasminogen activator inhibitor-1 (PAI-1) and fibronectin 1 (FN-1) playing important roles in these pathogenic processes. To investigate whether the plant metabolite curcumin, which exerts epigenetic modulatory properties when applied as a pharmacological agent, may prevent DN via inhibition of the JNK pathway and epigenetic histone acetylation, diabetic and age-matched non-diabetic control mice were administered a 3-month course of curcumin analogue (C66), c-Jun N-terminal kinase inhibitor (JNKi, sp600125), or vehicle alone. At treatment end, half of the mice were sacrificed for analysis and the other half were maintained without treatment for an additional 3months. Renal JNK phosphorylation was found to be significantly increased in the vehicle-treated diabetic mice, but not the C66- and JNKi-treated diabetic mice, at both the 3-month and 6-month time points. C66 and JNKi treatment also significantly prevented diabetes-induced renal fibrosis and dysfunction. Diabetes-related increases in histone acetylation, histone acetyl transferases' (HATs) activity, and the p300/CBP HAT expression were also significantly attenuated by C66 or JNKi treatment. Chromatin immunoprecipitation assays showed that C66 and JNKi treatments decreased H3-lysine9/14-acetylation (H3K9/14Ac) level and p300/CBP occupancy at the CTGF, PAI-1 and FN-1 gene promoters. Thus, C66 may significantly and persistently prevent renal injury and dysfunction in diabetic mice via down-regulation of diabetes-related JNK activation and consequent suppression of the diabetes-related increases in HAT activity, p300/CBP expression, and histone acetylation.

Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

BackgroundMany noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown.ResultsTo gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains.ConclusionHCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.

Abstract SY04-02: Dietary fiber protects against colorectal tumorigenesis in a microbiota- and butyrate-dependent manner

Abstract It is controversial whether dietary fiber protects against colorectal cancer because of conflicting results from human epidemiologic studies. These studies have been complicated by the participants’ genetic heterogeneity and differences in the composition of microbiota within their gastrointestinal tracts. To eliminate these confounding variables, we utilized a gnotobiotic mouse model of colorectal cancer. Our experiments were designed to investigate the function of butyrate because it is a short-chain fatty acid produced by bacterial fermentation of fiber in the colon at high (mM) levels and has potent energetic and epigenetic properties in host colonocytes. Here, we report that fiber did, in fact, have a chemoprotective effect but in a microbiota- and butyrate-dependent manner. The incidence, number, size, and histopathologic progression of AOM/DSS-induced colorectal tumors were significantly diminished when BALB/c mice were provided a high-fiber diet only if they were colonized with defined microbiota that included a butyrate-producing bacteria. This chemoprotective effect was attenuated when mice were colonized with the same microbiota except that the wild-type butyrate producer was replaced by a mutant strain with a 0.8-kb deletion in the butyryl-CoA synthesis operon. To confirm that butyrate is a causal factor, the chemoprotective effect was recapitulated in mice without any butyrate-producing bacteria if they were provided a butyrate-fortified diet. Our data support a general mechanism that includes microbial fermentation of fiber rather than fiber exclusively speeding colonic transit to minimize the exposure of colonocytes to ingested carcinogens. Our data also support a molecular mechanism that is metaboloepigenetic. Normal colonocytes utilize butyrate as their preferred energy source, whereas cancerous colonocytes rely on glucose because of the Warburg effect. Due to this metabolic difference, butyrate accumulated in tumors (as measured by LC-MS) and functioned as an HDAC inhibitor to increase histone acetylation levels and apoptosis. To support the applicability of this model to human cancer, we demonstrate that butyrate also accumulates at higher levels in human colorectal tumors than in normal colonic tissue, and this is associated with higher levels of histone acetylation in tumors. These results link diet and microbiota to a common metabolite that influences epigenetics and cancer predisposition. Citation Format: Dallas Donohoe, Darcy Holley, Leonard Collins, Stephanie Montgomery, Alan Whitmore, Andrew Hillhouse, Kaitlin Curry, Sarah Renner, Alicia Greenwalt, Elizabeth Ryan, Virginia Godfrey, Mark Heise, Deborah Threadgill, James Swenberg, David Threadgill, Scott Bultman. Dietary fiber protects against colorectal tumorigenesis in a microbiota- and butyrate-dependent manner. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY04-02. doi:10.1158/1538-7445.AM2014-SY04-02

Study of epigenetic properties of Poly(HexaMethylene Biguanide) hydrochloride (PHMB).

Poly(HexaMethylene Biguanide) hydrochloride (PHMB) CAS No. [32289-58-0] is a particularly effective member of the biguanides antiseptic chemical group, and has been in use since the early fifties in numerous applications. It has been proposed that PHMB be classified as a category 3 carcinogen although PHMB is not genotoxic. It has been hypothesized that PHMB may have epigenetic properties effects, including non-genotoxic modifications of DNA bases, DNA methylation and mitogenic cytokine production. These properties have been assessed in vitro using 3 cell types: Caco-2 cells (from a human colon adenocarcinoma) with a non-functional p53 gene. (∆p53: mut p53), N2-A (Neuro-2A cells, mouse neural cells), the brain being a possible target organ in rodents and HepG2 cells (human hepatocellular carcinoma) with functional p53 gene. From the concentration 1 μg/mL up to 20 μg/mL of PHMB, no effect was observed, either growth stimulation or inhibition. Viability testing using neutral red led to an IC 50 of 20–25 μg/mL after treatment with PHMB for 3 h, whereas the MTT test led to IC50 values of 80 μg/mL, 160 μg/mL and 160 μg/mL respectively for HepG2 cells, Neuro-2A cells and Caco-2 cells. PHMB does not induce significant oxidative stress (production of MDA or lipoperoxidation, nor does it induce hydroxylation of DNA (8-OH-dG) and/or its hypermethylation (m5dC), the latter being strongly implicated in DNA replication and regulation and cell division. PHMB does not induce significant production of mitogenic cytokines such as TNF-α (tumor necrosis factor), interleukins (IL-1 alpha), and the transcription factor nuclear factor kappa B (NF-κB) which can cause either apoptosis or stimulate the growth of transformed cells or tumors. Instead, from concentrations of 20 to 100 μg/mL, PHMB kills cells of all types in less than 3 h. The expression of genes involved in the mechanisms of cell death induced by PHMB, including p53, the pro apoptotic gene bax and others, the anti-apoptotic bcl-2 and caspase-3 has been evaluated by RT-PCR. Finally, the status of GAP-junctions (GJIC) in the presence of PHMB has been determined and appeared to not be significantly affected. Taken together the data show that in vitro PHMB does not exhibit clear and remarkable epigenetic properties except a slight increase of some cytokines and transcription factor at higher concentrations at which cell lysis occurs rapidly.

Evaluation of epigenetic properties of dioscin and diosgenin isolated from wild yam (Dioscorea villosa) root extract

Evaluation of epigenetic properties of dioscin and diosgenin isolated from wild yam (Dioscorea villosa) root extract

Epigenetic impact of curcumin on stroke prevention.

The epigenetic impact of curcumin in stroke and neurodegenerative disorders is curiosity-arousing. It is derived from Curcuma longa (spice), possesses anti-oxidative, anti-inflammatory, anti-lipidemic, neuro-protective and recently shown to exhibit epigenetic modulatory properties. Epigenetic studies include DNA methylation, histone modifications and RNA-based mechanisms which regulate gene expression without altering nucleotide sequences. Curcumin has been shown to affect cancer by altering epigenetic changes but its role as an epigenetic agent in cerebral stroke has not been much explored. Although curcumin possesses remarkable medicinal properties, the bioavailability of curcumin has limited its success in epigenetic studies and clinical trials. The present review is therefore designed to look into epigenetic mechanisms that could be induced with curcumin during stroke, along with its molecular designing with different moieties that may increase its bioavailability. Curcumin has been shown to be encapsulated in exosomes, nano-vesicles (<200 nm), thereby showing its therapeutic effects in brain diseases. Curcumin delivered through nanoparticles has been shown to be neuroregenerative but the use of nanoparticles in brain has limitations. Hence, curcumin-encapsulated exosomes along with curcumin-primed exosomes (exosomes released by curcumin-treated cells) are much needed to be explored to broadly look into their use as a novel therapy for stroke.

Genome wide DNA methylation profiling of osteoarthritic articular cartilage

s / Osteoarthritis and Cartilage 22 (2014) S7–S56 S41 CpG dinucleotides differs substantially between hips and knees, generic OA related differential methylation was observed in both hips and knees. Furthermore, we show that mere methylation differences do not imply gene regulation and therefore do not per se elucidate epigenetic regulatory properties of OA associated genes. Finally, gene set enrichment revealed that in late-stage disease extracellular matrix remodelling associated genes are still actively regulated epigenetically. 62 NOVEL VARIANTS FOR CARTILAGE THICKNESS AND HIP OSTEOARTHRITIS: REVEALING GENES IMPLICATED IN CARTILAGE AND BONE DEVELOPMENT M. Castano-Betancourt y, D. Evans z, Y. Liu x, M. Yau k, A. Uitterlinden y, V. Evangelou{, T. Spector#, M. Kloppenburg yy, M. Doherty zz, E. Waarsing y, V. Kraus xx, J. Jordan xx, F. Lafeber kk, B. Mitchell k, I. Meulenbelt yy, N. Lane{{, A. Valdes zz, J. van Meurs y. y ErasmusMC, Rotterdam, Netherlands; zCalifornia Pacific Med. Ctr. Res. Insitute, San Francisco, CA; x Thurston Arthritis Res. Ctr., Chapel Hill, NC, USA; kUniv. of Maryland Sch. of Med., Baltimore, MD, USA; {Univ. of Ioannina Med. Sch., Ioannina, Greece; Kings Coll., London, United Kingdom; yy Leiden Univ. Med. Ctr., Leiden, Netherlands; zzUniv. of Nottingham, Nottingham, United Kingdom; xxDuke Univ. Med. Ctr., Durham, NC, USA; kkUtrecht Univ., Utrecht, Netherlands; {{California Pacific Med. Ctr. Res. Inst., San

An evaluation of a SVA retrotransposon in the FUS promoter as a transcriptional regulator and its association to ALS.

Genetic mutations of FUS have been linked to many diseases including Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration. A primate specific and polymorphic retrotransposon of the SINE-VNTR-Alu (SVA) family is present upstream of the FUS gene. Here we have demonstrated that this retrotransposon can act as a classical transcriptional regulatory domain in the context of a reporter gene construct both in vitro in the human SK-N-AS neuroblastoma cell line and in vivo in a chick embryo model. We have also demonstrated that the SVA is composed of multiple distinct regulatory domains, one of which is a variable number tandem repeat (VNTR). The ability of the SVA and its component parts to direct reporter gene expression supported a hypothesis that this region could direct differential FUS expression in vivo. The SVA may therefore contribute to the modulation of FUS expression exhibited in and associated with neurological disorders including ALS where FUS regulation may be an important parameter in progression of the disease. As VNTRs are often clinical associates for disease progression we determined the extent of polymorphism within the SVA. In total 2 variants of the SVA were identified based within a central VNTR. Preliminary analysis addressed the association of these SVA variants within a small sporadic ALS cohort but did not reach statistical significance, although we did not include other parameters such as SNPs within the SVA or an environmental factor in this analysis. The latter may be particularly important as the transcriptional and epigenetic properties of the SVA are likely to be directed by the environment of the cell.

Selecting T-Cell Subsets for Adoptive T-Cell Therapy to Optimize Potency and Persistence

Adoptive T-cell therapy with tumor-reactive T cells is emerging as a highly effective strategy for eliminating even the most advanced chemotherapy refractory malignancies. Endogenous T cells specific for tumor-associated antigens can sometimes be isolated and expanded from the patient's blood or tumor infiltrate, or more expeditiously can be engineered by gene transfer to express a T-cell receptor specific for a tumor associated MHC/peptide complex or a synthetic chimeric antigen receptor (CAR) specific for a tumor associated cell surface molecule. The remarkable regression of advanced acute lymphocytic leukemia and lymphoma in patients treated with T cells engineered to express CD19-specific CARs illustrates the potential for this approach to transform clinical care. Therapeutic activity is variable in individual patients, however, and this appears to correlate with the ability of transferred, tumor-reactive T cells to persist and proliferate in vivo, and to retain effector function. These attributes may reflect both the qualities of the T cells that are isolated or engineered for therapy, and the local tumor microenvironment that may contain regulatory T cells; cells that express ligands that engage inhibitor receptors on effector T cells or cytokines that inhibit effector T-cell proliferation. The CD4+ and CD8+ T cell pools in normal individuals contain a variety of naïve, memory, and regulatory T-cell subsets that differ in epigenetic, transcriptional, and functional properties. Because most clinical protocols have used polyclonal peripheral blood mononuclear cells as recipients for CAR gene transfer, the composition of T-cell products that are being administered is highly variable, particularly when the T cells are obtained from cancer patients that have received prior cytotoxic chemotherapy that can skew the phenotypic composition of the peripheral T-cell pool. As a consequence, transferring tumor-targeting receptors into polyclonal unselected cell populations provides poor control over the cellular composition of the final T-cell product, which may in part explain the marked differences in efficacy and toxicity that have been observed in the clinic, and may complicate regulatory approval of these novel therapies. Methods to derive T cells from distinct naïve and memory T-cell subsets have been developed, enabling the rapid production of therapeutic T cells of uniform composition. The results of preclinical studies that illustrate the improved potency of defined T-cell products that are engineered with tumor-specific CARs, and the clinical implementation of this approach in B-cell malignancies will be presented. Disclosures:Riddell:Cell Medica: Consultancy, Membership on an entity's Board of Directors or advisory committees; ZetaRx: Consultancy.

Threonine metabolism and embryonic stem cell self-renewal

Embryonic stem cells (ESCs) undergo unlimited self-renewal while maintaining a pluripotency, which is defined as the ability to develop into cells of all three embryonic germ layers. ESC self-renewal is characterized by special proliferative and epigenetic properties and a unique metabolic profile. One of the key features of this specialized nutritional metabolism is a stringent requirement for the amino acid threonine. Until recently, little was known about amino acid metabolism in stem cells beyond their general role in protein synthesis. Recent findings demonstrating a central role for threonine metabolism in multiple aspects of stem cell biology will be presented in this review. Amino acid catabolism supplies essential building blocks for biosynthetic pathways and for chemical modification of chromatin. In a series of recent studies employing combinative approaches of metabolomics, nutrition and genetics, the amino acid threonine was identified as an essential nutrient for mouse ESC (mESC). An unexpected finding from these studies was that in addition to its well known importance as protein precursor, threonine dehydrogenase-mediated threonine catabolism provides essential metabolic building blocks for use in multiple biosynthetic pathways and epigenetic modifications required for self-renewal and maintenance of pluripotency. Recent studies on threonine catabolism in mESCs suggest that amino acids can play both powerful biosynthetic and signaling roles in stem cells. These results described in mESCs should stimulate a new research area on the effect of amino acid metabolism in stem cell self-renewal and differentiation.

Derivation of novel human ground state naive pluripotent stem cells

Mouse embryonic stem (ES) cells are isolated from the inner cell mass of blastocysts, and can be preserved in vitro in a naive inner-cell-mass-like configuration by providing exogenous stimulation with leukaemia inhibitory factor (LIF) and small molecule inhibition of ERK1/ERK2 and GSK3β signalling (termed 2i/LIF conditions). Hallmarks of naive pluripotency include driving Oct4 (also known as Pou5f1) transcription by its distal enhancer, retaining a pre-inactivation X chromosome state, and global reduction in DNA methylation and in H3K27me3 repressive chromatin mark deposition on developmental regulatory gene promoters. Upon withdrawal of 2i/LIF, naive mouse ES cells can drift towards a primed pluripotent state resembling that of the post-implantation epiblast. Although human ES cells share several molecular features with naive mouse ES cells, they also share a variety of epigenetic properties with primed murine epiblast stem cells (EpiSCs). These include predominant use of the proximal enhancer element to maintain OCT4 expression, pronounced tendency for X chromosome inactivation in most female human ES cells, increase in DNA methylation and prominent deposition of H3K27me3 and bivalent domain acquisition on lineage regulatory genes. The feasibility of establishing human ground state naive pluripotency in vitro with equivalent molecular and functional features to those characterized in mouse ES cells remains to be defined. Here we establish defined conditions that facilitate the derivation of genetically unmodified human naive pluripotent stem cells from already established primed human ES cells, from somatic cells through induced pluripotent stem (iPS) cell reprogramming or directly from blastocysts. The novel naive pluripotent cells validated herein retain molecular characteristics and functional properties that are highly similar to mouse naive ES cells, and distinct from conventional primed human pluripotent cells. This includes competence in the generation of cross-species chimaeric mouse embryos that underwent organogenesis following microinjection of human naive iPS cells into mouse morulas. Collectively, our findings establish new avenues for regenerative medicine, patient-specific iPS cell disease modelling and the study of early human development in vitro and in vivo.

노화 관련 유전자의 후성유전학적 특성 분석

Gene expression is regulated by a wide range of mechanisms at the DNA sequence level. In addition, gene expression is also regulated by epigenetic mechanisms through DNA methylation, histone modification, and ncRNA. To understand the regulation of gene expression at the epigenetic level, we constructed aging related gene database and analyzed epigenetic properties that are focused on DNA methylation. The DNA methylation of promoter or upstream region of the genes induces to repress the gene expression. We compared and analyzed distribution between whole human genes and aging related genes in the epigenetic properties such as CGI distribution, methylation motif pattern, and TFBS (transcription factor binding site) distribution. In contrast to methylation motif pattern, CGI and TFBS distributions are positively correlated with epigenetic regulation of aging related gene expression. In this study, the epigenetic data about DNA methylation of the aging genes will provide us to understand phenomena of the aging and epigenetic mechanism for regulation of aging related genes.

The impact of culture on epigenetic properties of pluripotent stem cells and pre-implantation embryos

Cultured pluripotent stem cells hold great promise for regenerative medicine. Considerable efforts have been invested into the refinement and definition of improved culture systems that sustain self-renewal and avoid differentiation of pluripotent cells invitro. Recent studies have, however, found that the choice of culture condition has a significant impact on epigenetic profiles of cultured pluripotent cells. Mouse and human ESCs (embryonic stem cells) show substantial epigenetic differences that are dependent on the culture condition, including global changes to DNA methylation and histone modifications and, in female human ESCs, to the epigenetic process of X chromosome inactivation. Epigenetic perturbations have also been detected during culture of pre-implantation embryos; limited research undertaken in mouse suggests a direct effect of the invitro environment on epigenetic processes in this system. Widespread epigenetic changes induced by the culture condition in stem cells thus emphasize the necessity for extensive research into both immediate and long-term epigenetic effects of embryo culture during assisted reproductive technologies.

Induced Pluripotent Stem Cells (iPSCs) Derived from Different Cell Sources and their Potential for Regenerative and Personalized Medicine

Human induced pluripotent stem cells (hiPSCs) have great potential as a robust source of progenitors for regenerative medicine. The novel technology also enables the derivation of patient-specific cells for applications to personalized medicine, such as for personal drug screening and toxicology. However, the biological characteristics of iPSCs are not yet fully understood and their similarity to human embryonic stem cells (hESCs) is still unresolved. Variations among iPSCs, resulting from their original tissue or cell source, and from the experimental protocols used for their derivation, significantly affect epigenetic properties and differentiation potential. Here we review the potential of iPSCs for regenerative and personalized medicine, and assess their expression pattern, epigenetic memory and differentiation capabilities in relation to their parental tissue source. We also summarize the patient-specific iPSCs that have been derived for applications in biological research and drug discovery; and review risks that must be overcome in order to use iPSC technology for clinical applications.

Abstract SY08-03: Metaboloepigenetic effects of microbial-produced butyrate in cancer prevention.

Abstract It is controversial whether dietary fiber protects against colorectal cancer because of conflicting results from human epidemiologic studies. These studies have been complicated by the participants' genetic heterogeneity and differences in the composition of microbiota within their gastrointestinal tracts. To eliminate these confounding variables, we utilized a gnotobiotic mouse model of colorectal cancer. Our experiments were designed to investigate the function of butyrate because it is a short-chain fatty acid produced by bacterial fermentation of fiber in the colon at high (mM) levels and has potent energetic and epigenetic properties in host colonocytes. Here, we report that fiber did, in fact, have a chemoprotective effect but in a microbiota- and butyrate-dependent manner. The incidence, number, size, and histopathologic progression of AOM/DSS-induced colorectal tumors were significantly diminished when BALB/c mice were provided a high-fiber diet only if they were colonized with defined microbiota that included a butyrate-producing bacteria. This chemoprotective effect was attenuated when mice were colonized with the same microbiota except that the wild-type butyrate producer was replaced by a mutant strain with a 0.8-kb deletion in the butyryl-CoA synthesis operon. To confirm that butyrate was a causal factor, the chemoprotective effect was also observed in mice without any butyrate-producing bacteria if their diet was fortified with a butyrate derivative. Our data support a general mechanism that includes microbial fermentation of fiber rather than fiber exclusively speeding colonic transit to minimize the exposure of colonocytes to ingested carcinogens. Our data also support a molecular mechanism that is metaboloepigenetic. Normal coloncytes utilize butyrate as their preferred energy source, whereas cancerous colonocytes rely on glucose because of the Warburg effect. Due to this metabolic difference, butyrate accumulated in tumors (as measured by LC-MS/MS) and functioned as an HDAC inhibitor to increase global histone acetylation levels and apoptosis. To support the applicability of this model to human cancer, we demonstrate that butyrate also accumulates at higher levels in human colorectal tumors than in normal colonic tissue, and this is associated with higher levels of histone acetylation in tumors. These results link diet and microbiota to a common metabolite that influences epigenetics and cancer predisposition. To investigate the metaboloepigenetic mechanism in more detail, we evaluated the effect of butyrate in colorectal cancer cell lines in the presence of the Warburg effect and when it was prevented from occurring by growing the tumor cells in low glucose or depleting lactate dehydrogenase levels (siLDHA). Low doses of butyrate (0.5-1 mM) inhibited cell proliferation in the presence of the Warburg effect by acting as an epigenetic factor (by inducing histone acetylation) but stimulated proliferation in the absence of the Warburg effect by acting as an energy source. Low doses of butyrate also stimulated the proliferation of non-cancerous colonocytes, which do not undergo the Warburg effect without any experimental manipulation. Higher doses of butyrate (2-5 mM), which exceed the metabolic capacity of the cell to oxidize butyrate (but are still physiologically relevant), induced histone acetylation and apoptosis regardless of the Warburg effect. At the lower doses, where butyrate was metabolized, it was converted to acetyl-CoA, and this was important not only for energetics but also for epigenetics because it served as a HAT co-factor to stimulate histone acetylation. Although the acetyl-CoA/HAT and HDAC inhibition mechanisms both stimulate histone acetylation, they were differentially utilized and upregulated different target genes. The acetyl-Co-A/HAT mechanism was predominant in normal cells and at low butyrate doses regardless of the Warbug effect and upregulated cell proliferation genes, whereas the HDAC inhibition mechanism was predominant in cancerous colonocytes and at high butyrate doses regardless of the Warburg effect and upregulated pro-apoptotic genes. These data have important implications in vivo. Because mucus produced by goblet cells within the crypts flows upward into the lumen, an endogenous butyrate gradient is believed to exist with lower concentrations at the base of crypts (&amp;lt;1 mM) than in the lumen (2-5 mM). Therefore, butyrate may contribute to normal colonic homeostasis by promoting the proliferation of stem cells and transit amplifying cells near the base while inducing apoptosis in cells exfoliating into the lumen. And due to the Warburg effect in tumor cells, butyrate is not readily metabolized, accumulates, and functions primarily as an HDAC inhibitor regardless of position within the epithelium. These results indicate that metabolic transformation (i.e., the Warburg effect) can drive aberrant epigenetic (histone acetylation) and transcriptome profiles in tumor cells compared to their cell of origin. Citation Format: Dallas Donohoe, Stephanie Montgomery, Leonard Collins, Darcy Holley, Virgina Godfrey, James Swenberg, Scott Bultman. Metaboloepigenetic effects of microbial-produced butyrate in cancer prevention. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY08-03. doi:10.1158/1538-7445.AM2013-SY08-03

Abstract SY03-01: Genotypic and phenotypic features of de novo and acquired resistance to cancer therapies.

Abstract Drug resistance is the single cause of cancer treatment failure resulting in cancer related death. Despite its paramount importance, our mechanistic understanding and means of circumventing cancer drug resistance is limited. In the current era, the evolutionary processes in cancer development and progression have been elucidated and provide insights into the biology of cancer and in particular cancer heterogeneity. However, our understanding of the contribution of evolutionary processes and tumor heterogeneity to the development of drug resistance is limited. As a result, our ability to translate knowledge into effective clinical strategies is similarly limited and remains largely on the use combination chemotherapy based on Goldie and Coldman's principles first described in 1984. Pragmatically, resistance may be de novo (i.e. treatment has no effect) or acquired (i.e. treatment had initial effect but tumors eventually progress due to repopulation by resistant cells). De novo resistance is thus equivalent to primary refractoriness and acquired resistance is emergent in the presence and presumably as a direct response to the selective pressures imposed by therapy. Mechanisms of resistance may be divided into various categories; however, a simple construct is to consider resistance as a manifestation of failure of one or more of the following: drug delivery, drug uptake, drug-target interaction and cellular response and cellular adaptation. Genetic, epigenetic, physiochemical and spatial properties of cancers may contribute to drug resistance and it is likely that different mechanisms of drug resistance develop concomitantly. The most important challenge is how to tackle the interrelated problems of tumor genetic and epigenetic heterogeneity and drug resistance in cancer using rational drug selections. The identification of tumor dependencies driven by dominant oncogenes, hormones, or metabolites may prove vulnerable to regimens designed to intercept them assuming dependencies are identifiable, targets or target pathways are “druggable” and such agents and combinations are tolerable and effective for cancer patients. Although the issues are complex, they can and should be addressed. Serial and comprehensive sampling to identify genetic and epigenetic changes of tumor to guide drug therapy will be required as will identifying susceptibilities such as oncogene addiction, synthetic lethality and genomic instability. Rational selection of drug dose, schedule and combination partners can follow. Treatment advances will occur to the extent that mechanisms of resistance can be identified or predicted and circumvented. Citation Format: Janet E. Dancey. Genotypic and phenotypic features of de novo and acquired resistance to cancer therapies. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY03-01. doi:10.1158/1538-7445.AM2013-SY03-01

Differentiation of developing olfactory neurons analysed in terms of coupled epigenetic landscapes.

The olfactory system integrates signals from receptors expressed in olfactory sensory neurons. Each sensory neuron expresses only one of many similar olfactory receptors (ORs). The choice of receptor is made stochastically early in the differentiation process and is maintained throughout the life of the neuron. The underlying mechanism of this stochastic commitment to one of multiple similar OR genes remains elusive. We present a theoretical analysis of a mechanism that invokes important epigenetic properties of the system. The proposed model combines nucleosomes and associated read–write enzymes as mediators of a cis-acting positive feedback with a trans-acting negative feedback, thereby coupling the local epigenetic landscape of the individual OR genes in a way that allow one and only one gene to be active at any time. The model pinpoint that singular gene selection does not require transient mechanisms, enhancer elements or transcription factors to separate choice from maintenance. In addition, our hypothesis allow us to combine all reported characteristics of singular OR gene selection, in particular that OR genes are silenced from OR transgenes. Intriguingly, it predicts that OR transgenes placed in close proximity should always be expressed simultaneously, though rarely.

A comparison of pluripotency and differentiation status of four mesenchymal adult stem cells

The self-renewal and differentiation status of a stem cell is very important in the applications concerning regenerative medicine. Proliferation capacity, differentiation potentials and epigenetic properties of stem cells differ between sources. Studies have shown the high potentials of stem cells in iPS reprogramming. To examine this; we have compared the stem-ness and differential potential of four adult stem cells from common sources. We show a correlation between pluripotency and differentiation status of each stem cell with available data on the reprogramming efficiency. Four human adult stem cells including, adipose tissue-mesenchymal stem cells (AT-MSC), bone marrow mesenchymal stem cells (BM-MSCs), nasal septum derived multipotent progenitors (NSP) and umbilical cord blood stem cells (USSCs) were isolated and characterized. The self- renewal and differentiation potentials of each stem cell were assessed. Stem-ness transcription factors and the propagation potentials of all cells were analyzed. Furthermore the differentiation potentials were evaluated using treatment with induction factors and specific MicroRNA profile. Real-time PCR results showed that our stem cells express innate differentiation factors, miR145 and Let7g, which regulate the stem-ness and also the reprogramming potentials of each stem cell. To complete our view, we compared the propagation and differentiation potentials by correlating the stem-ness gene expression with differentiation MicroRNAs, also the direct effect of these factors on reprogramming. Our results suggest that the potentials of adipose tissue stem cells for GMP (Good Manufacturing Practice) compliant starting material are adequate for clinical applications. Our results indicate a low risk potential for AT-MSCs as starting material for iPS production. Although let7g and mir145 are well known for their differentiation promoting effects, but function more of a fine tuning system between self-renewal and differentiation status.

Epigenetic effects of nano-sized materials

The term epigenetics includes several phenomena such as DNA methylation, histone tail modifications, and microRNA mediated mechanisms, which are able to mold the chromatin structure and/or gene expression levels, without altering the primary DNA sequence. Environmental agents can exert epigenetic properties and there is increasing evidence of epigenetic deregulation of gene expression in several human diseases, including cancer, cardiovascular diseases, autism spectrum disorders, autoimmune diseases, and neurodegeneration, among others. Given the widespread use and dispersion in the environment of nano-sized materials, this article summarizes the studies performed so far to evaluate their potential epigenetic properties. Those studies highlight the ability of certain nano-sized compounds to induce an impaired expression of genes involved in DNA methylation reactions leading to global DNA methylation changes, as well as changes of gene specific methylation of tumor suppressor genes, inflammatory genes, and DNA repair genes, all potentially involved in cancer development. Moreover, some nano-sized compounds are able to induce changes in the acetylation and methylation of histone tails, as well as microRNA deregulated expression. We also provided a detailed description of currently available methodologies to evaluate epigenetic modifications. Standard protocols are currently available to evaluate cytotoxic and genotoxic effects of nano-sized materials. By contrast, there are at present no available standard protocols to evaluate the epigenetic potential of any given compound. The currently available methodologies offer different, but often complementary information to characterize potential epigenetic changes induced by exposure to nano-sized compounds. Given the widespread use and dispersion in the environment of nano-sized materials, at present and foreseeable in the near future, and in light of the indication of potential epigenetic properties here reviewed, more attention should be paid to unravel the consequences of such effects in future studies.

Establishment of a New Mantle Cell Lymphoma Cell Line That Has Epigenetically Silenced CD20 As a Resistance Mechanism in Vivo

AbstractAbstract 4619Rituximab is an anti-CD20 monoclonal antibody that has significant activity in B cell lymphomas that express the cell surface protein CD20. The mechanism of its antitumor effects in vivo are not clear but include direct apoptotic effects, complement mediated cytotoxicity (CMC), and antibody dependent cellular cytotoxicity (ADCC). Previously we initiated a clinical trial of SAHA (vorinostat), cladribine, and rituximab (SCR) in patients with CD20+ B cell malignancies. In addition to its cytotoxic effects, recent evidence suggests that 2-CdA has hypomethylating properties.A 65 year old patient with newly diagnosed blastic,leukemic, mantle cell lymphoma (MCL) was initiated on the SCR trial. He responded promptly with normalization of his blood counts and resolution of his splenomegaly. A PET/CT scan performed prior to cycle 3 was consistent with a complete metabolic remission. He developed cytopenias prior to cycle 5 that met criteria for removal from the study. Imaging and blood studies were compatible with florid relapse of his MCL including CNS disease. At post mortem analysis, cells in the CNS were CD20 positive and cells in the blood, marrow, and lymph nodes were CD20 negative by immunohistochemistry and flow cytometry. CD20 mRNA analysis by qRT-PCR demonstrated marked reduction in CD20 mRNA. A cell line was derived from the patient’s blood. The cells are cyclin D1 positive and expresses Sox 11 with ∼50 times less CD20 mRNA and appropriate sized protein. This 353 cell line has been grown in continuous culture for > 1 year and remains CD20 negative, CCND1 positive and contains the t(11;14). Analysis of the CD20 promoter and coding region demonstrated no evidence of a deletion or point mutation.Chromatin immunoprecipation (ChIP) assays were performed to access epigenetic changes at the CD20 promoter. First, we showed that the CD20 promoter in Granta MCL cells treated with cladribine contain decreased amounts of methylated histones H3K9 and K27, consistent with an epigenetic mechanism of action of cladribine involving histone methylation. Decreased DNA methylation at the CD20 promoter was also observed.ChIP analysis of the patient's cells before and after treatment with cladribine and vorinostat in vivo demonstrated decreases in CD20 promoter DNA and histone (H3 K9 and H3K27) methylation, consistent with the known epigenetic properties of these agents.The 353 cell line reported here will be of interest in studying epigenetic mechanisms of resistance to rituximab by silencing of CD20 gene expression. Experiments to overexpress exogenous CD20 to resensitize 353 cells to rituximab are in progress and will be reported. Future experiments will also aim at identifying a cDNA or drug that can overcome epigenetic resistance in vitro in 353 cells. These experiments could lead to improved treatments to overcome epigenetically mediated resistance to rituximab. Disclosures:No relevant conflicts of interest to declare.