bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A13: Androgen receptor functions as an adaptor protein for recruitment of protein phosphatase 1a to chromatin and CDK9 mobilization
Authors: Liu Xiaming , Gao Yanfei , Cai Changmeng , Balk Steven , Chen Shaoyong
Published: May 2016

The androgen receptor (AR) plays a central role in prostate cancer (PCa) development and progression. AR activity can be modulated by phosphorylation at multiple sites, with S81 phosphorylation mediated by CDK9 playing a particularly important role that may be due to enhancing recruitment of the coactivator p300. The CDK9/cyclin T complex (P-TEFb) is recruited to enhancer/promoter sites by BRD4, where it phosphorylates NELF and RNA polymerase 2 to stimulate transcriptional elongation. A large fraction of P-TEFb is held in an inactive state by association with a 7SK RNA complex, and can be released from this complex through dephosphorylation of CDK9 by protein phosphatase 1 (PP1). The major isoform of the PP1 catalytic subunit, PP1a, associates with a large number of regulatory proteins that target it to specific sites. PNUTS is a regulatory protein targeting PP1a to chromatin, but additional mechanisms that may target PP1a to chromatin to mediate CDK9 dephosphorylation and drive transcriptional elongation remain to be identified. We reported previously that AR could interact with PP1a, and that PP1a could enhance AR activity by dephosphorylating S650 in the AR hinge region and thereby prevent its nuclear export. In this study we show by chromatin immunoprecipitation that AR also recruits PP1a to androgen-stimulated enhancers, and show that PP1a inhibition with tautomycin prevents P-TEFb recruitment to AR-regulated genes and CDK9-mediated phosphorylation of RNA polymerase 2. We further show that PP1a binds to the AR ligand binding domain independently of ligand, and that this binding is negatively regulated by the androgen induced AR N/C-terminal interaction. Significantly, the AR N/C interaction impairs AR recruitment of coactivators prior to chromatin binding, but is disrupted on chromatin to enhance coactivator recruitment, which would also facilitate recruitment of PP1a. These findings indicate that AR functions as a PP1a regulatory protein targeting PP1a to chromatin, and thereby identify a novel mechanism for the selective recruitment of PP1a to a specific subset of genes where it can drive transcriptional elongation, and may also regulate mRNA splicing.

Citation Format: Xiaming Liu, Yanfei Gao, Changmeng Cai, Steven Balk, Shaoyong Chen. Androgen receptor functions as an adaptor protein for recruitment of protein phosphatase 1a to chromatin and CDK9 mobilization. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A13.
Abstract A21: The role of SOX4 in epithelial to mesenchymal transition in prostate cancer
Authors: Sharma Nitya V. , Sannigrahi Soma , Lai YuHeng , Moreno Carlos
Published: May 2016

Prostate cancer remains the most commonly diagnosed cancer in U.S. males, and ranks second in mortality with over 28,000 deaths per year. Prostate cancer mortality is typically due to metastases, necessitating the understanding of how metastatic disease develops. One major step for cancer cells to metastasize and acquire migratory and invasive capabilities is the epithelial to mesenchymal transition (EMT). EMT encompasses vast molecular changes in gene expression, mediated by aberrant developmental signaling pathway activation, leading to the loss of cell-cell junctions and planar and apical-basal polarity, increased motility, and resistance to apoptosis and anoikis (cell death due to the detachment from the extracellular matrix). The sex determining region Y-box 4 (SOX4) gene is a developmental transcription factor that is over expressed in prostate cancer and plays a critical role in many developmental pathways inappropriately activated during EMT, such as the transforming growth factor (TGF-beta) and epidermal growth factor receptor (EGFR) signaling pathways. Our data suggest that concomitant treatment of TGF-beta and EGF induces SOX4, and initiates the EMT program in prostate epithelial cell lines. We also demonstrate that SOX4 over expression is sufficient to induce EMT in prostate epithelial cell lines. Currently, the molecular mechanisms that govern how SOX4 initiates EMT via transcriptional activation of target genes are poorly understood. We identified candidate SOX4 targets using the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) on 9755 Pan Cancer samples from The Cancer Genome Atlas (TCGA). Gene ontology analysis of the top 1000 candidate SOX4 targets revealed genes that were enriched for epigenetic processes such as chromatin modification and DNA methylation. One putative target gene, PCAF, is a subunit of a large histone acetyltransferase (HAT) complex. Interestingly, our preliminary data also suggest that SOX4 interacts not only with PCAF, but also with TRRAP, another subunit of the PCAF HAT complex. These data suggest that SOX4 may induce and recruit the PCAF/TRRAP HAT complex in order to transcriptionally activate downstream targets to initiate the EMT program.

Citation Format: Nitya V. Sharma, Soma Sannigrahi, YuHeng Lai, Carlos Moreno. The role of SOX4 in epithelial to mesenchymal transition in prostate cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A21.
Abstract A37: Aberrant DNA methylation of HTATIP2 and UCH-L1 as prognostic and predictive biomarkers for cholangiocarcinoma
Authors: Limpaiboon Temduang , Nanok Chaiyachet , Proungvitaya Siriporn , Jearanaikoon Patcharee , Pugkhem Ake , Puapairoj Anucha
Published: May 2016

Cholangiocarcinoma (CCA) is a malignancy of bile duct epithelial cell lining. In the past decade, the incidence and mortality rates of CCA have been increasing worldwide. The effective treatment modality for CCA is surgical resection. Adjuvant chemotherapy and/or radiotherapy are optional therapy for unresectable and postoperative CCA. Unfortunately, the responsiveness of CCA patients to chemotherapy was relatively low and 5-year survival rate was poor. We have analyzed data which were obtained from our previous study on methylation microarray based on chemotherapeutic drug resistance and found aberrant DNA methylation of genes related to chemotherapy. This present study aimed to quantitate DNA methylation levels of 10 candidate genes related to chemotherapy in 54 CCA and 19 normal adjacent tissues using methylation-sensitive high resolution melting (MS-HRM) analysis. The methylation level of each gene was statistically analyzed with clinical parameters. Genes with high methylation level were UCH-L1 and IRF4, and genes with moderate methylation were CCND2, HTATIP2 and TP53I3. We found significant difference in methylation levels of HTATIP2 (P=0.036) and UCH-L1 (P=0.012) between short and long survival groups. Patients with high methylation level of HTATIP2 and low methylation of UCH-L1 showed longer overall survival (P=0.03 and P=0.044, respectively). Interestingly, chemotherapeutic responders showed higher methylation level of HTATIP2 than non-responders (P=0.020), whereas no significant difference in UCH-L1 methylation level was observed between these two groups. The methylation levels of HTATIP2 and UCH-L1 were low in normal adjacent tissues. In patients who received chemotherapy, patients who had high methylation of HTATIP2 and low methylation of UCH-L1 showed longer overall survival (P<0.001 and P=0.041, respectively). Moreover, HTATIP2 methylation was associated with tumor progression in which lower methylation level was found in CCA patients with positive lymph node metastasis (P=0.029). In conclusion, our finding indicates the great value of DNA methylation levels of HTATIP2 and UCH-L1 as prognostic and predictive markers for CCA patients.

Citation Format: Temduang Limpaiboon, Chaiyachet Nanok, Siriporn Proungvitaya, Patcharee Jearanaikoon, Ake Pugkhem, Anucha Puapairoj. Aberrant DNA methylation of HTATIP2 and UCH-L1 as prognostic and predictive biomarkers for cholangiocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A37.
Abstract A43: DNA repair by non-homologous end joining induced gene silencing via DNA hypermethylation
Authors: Allen Brittany N. , Masternak Michal , Muller Mark
Published: May 2016

Double strand breaks (DSBs) in DNA are repaired throughout the cell cycle and in non-dividing cells by the error-prone process of non-homologous end joining (NHEJ). In order to evaluate expression of a gene following NHEJ repair, we use a GFP reporter system to allow for targeted induction of a DSB in the genome of Hela cells. Prior to induction of the DSB, GFP is transcribed but inactive due to an extra exon interrupting the gene sequence, however cells that successfully repair the DSB express WT GFP that can be detected by fluorescent based assays. Following repair, two different GFP expression classes can be detected by flow cytometry: one that expresses GFP robustly (‘bright') and one that expresses GFP at a lower level (‘dim'). This is surprising given that these experiments are done in a cell line derived from a single clone. This phenomenon was confirmed using live cell imaging. Treatment with a hypomethylating drug causes some ‘dim' cells to be converted to ‘bright' cells, suggesting that the gene silencing that occurs in the ‘dim' population is a result of hypermethylation of the gene. Bisulfite deep sequencing confirms that areas up- and downstream of the break site are hypomethylated in ‘bright' cell populations and hypermethylated in ‘dim' cell populations. It can be concluded from these data that, following repair of a DSB by NHEJ, the epigenetic landscape of the repaired gene, specifically the methylation status of its CpGs, is altered in a way that changes the expression levels of the repaired gene. Though their cause is not fully understood, gene expression changes caused by epigenetic reprogramming are a hallmark of many different types of cancer. Given the increased reliance of cancer cells on DNA repair, a link between epigenetic revision and DNA repair could provide an explanation for changes in the epigenome that occur during cancer progression.

Citation Format: Brittany N. Allen, Michal Masternak, Mark Muller. DNA repair by non-homologous end joining induced gene silencing via DNA hypermethylation. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A43.
Abstract A50: The identification of an Ets1-driven gene signature in head and neck squamous cell carcinoma
Authors: Gluck Christian , Sethi Isha , Tsompana Maria , Sinha Satrajit
Published: May 2016

Head and Neck Squamous Cell Carcinoma (HNSCC) is a heterogeneous disease of significant mortality and morbidity and with limited treatment options. This highlights the urgent need for a better understanding of the underlying biology of HNSCC. Recent genomic analysis of HNSCC tumors has identified four distinct molecular classes, of which the mesenchymal subtype is particularly aggressive in nature and associated with poor survival. We have discovered that Ets1, a prototypic oncogenic transcription factor, is selectively enriched in the mesenchymal HNSCC tumors along with other key drivers of Epithelial to Mesenchymal transition (EMT). Further analysis of gene expression datasets reveals that Ets1 expression, while low in normal epithelium, increases in pre-malignant and malignant tissues, suggesting a possible role for Ets1 during early tumorigenesis. Strikingly, Kaplan Meier analysis shows that Ets1 expression is associated with both poor survival in HNSCC and high incidence of tumor recurrence. We have performed hierarchical clustering of 33 HNSCC cell lines to show that these cell lines exhibit gene expression profiles that are representative of the four tumor subtypes. To better understand the Ets1-driven molecular processes in EMT high tumors, we have utilized SCC25, a mesenchymal HNSCC cell line to perform global transcriptomic analysis of effects of Ets1 knockdown. Additionally, we have also performed ChIP-seq experiments to identify genome wide transcriptional targets of Ets1 in SCC25. Taken together, these studies have uncovered an Ets1 intrinsic core gene signature that can serve as a valuable tool for further tumor classification and cancer-specific pathway discovery. Interestingly, by cross-referencing with the Cancer Genome Atlas HNSCC RNA-Seq dataset, we demonstrate that Ets1 expression is highly correlated with the majority of the Ets1 signature target genes thus reinforcing a functional relationship. Collectively, our findings not only identify several Ets1 dependent genes that are key to initiating and maintaining EMT in HNSCC, but also unearth novel targets that can be exploited for future therapeutics against this deadly cancer.

Citation Format: Christian Gluck, Isha Sethi, Maria Tsompana, Satrajit Sinha. The identification of an Ets1-driven gene signature in head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr A50.
Abstract B01: Biological consequences of histone mutations in the mammalian brain
Authors: Larson Jon D. , Kasper Lawryn H. , Russell Helen R. , Qu Chunxu , Zhu Xiaoyan , McKinnon Peter J. , Baker Suzanne J.
Published: May 2016

Pediatric high-grade gliomas (HGGs) are devastating diseases with poor prognosis. The two-year survival for pediatric HGG ranges from 30%, for tumors arising in the cerebral cortex, to less than 10% for diffuse intrinsic pontine gliomas (DIPGs), which arise in the brainstem. Recurrent somatic mutations in histone H3 found in pediatric HGGs are rare in adult HGGs and may represent genetic drivers of disease. Mutually exclusive somatic heterozygous H3F3A or HIST1H3B mutations encoding a K27M variant of histone H3.3 or H3.1, respectively, are found in nearly 80 percent of DIPGs and 22 percent of non-brainstem HGG, where they occur predominantly in thalamic and other midline tumors. Strikingly, heterozygous H3F3A mutations encoding histone H3.3 G34R or G34V occur in approximately 14 percent of non-brainstem HGG, and are associated predominantly with cortical tumors arising in older children through young adulthood, suggesting a distinct developmental origin compared to the majority of tumors harboring K27M mutations. DNA methylation signatures and gene expression patterns distinguish G34R/V and K27M tumors, but the oncogenic mechanisms and brain region selectivity of these mutations are still uncertain. To study these mutations in the developing mammalian brain, we generated conditionally activated, epitope tagged H3f3a knock-in mice to express K27M, G34R or non-mutated H3.3 proteins. When activated in neural and glial precursor cells, extensive H3f3a expression was observed throughout the embryonic brain, and H3.3-K27M induced loss of H3K27me3, consistent with observations in K27M mutant DIPG tumor samples. Moreover, neural stem cells expressing H3.3-K27M demonstrated an in vitro growth advantage compared to H3.3-G34R or H3.3-WT expressing neural stem cells. We will present an analysis of the epigenetic landscape and gene expression signatures associated with the histone H3 K27M and G34R mutations in different brain regions as well as phenotypic analysis of the mutant mice.

Citation Format: Jon D. Larson, Lawryn H. Kasper, Helen R. Russell, Chunxu Qu, Xiaoyan Zhu, Peter J. McKinnon, Suzanne J. Baker. Biological consequences of histone mutations in the mammalian brain. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B01.
Abstract B02: The role of chromatin remodeler protein ARID1a in ovarian clear cell carcinoma
Authors: Lakshminarasimhan Ranjani , Andreu-Vieyra Claudia , Lawrenson Kate , Gayther Simon A. , Jones Peter A. , Liang Gangning
Published: May 2016

Ovarian cancer is the fifth leading cause of cancer death among women in the United States and ovarian clear cell carcinoma (OCCC) is an aggressive subtype of epithelial ovarian cancer. Recent whole genome and whole exome sequencing studies have revealed that the chromatin remodeler protein AT-Rich Interactive Domain 1a (ARID1a) is frequently mutated in OCCC. ARID1a loss is also often observed in endometriosis which is strongly associated with OCCC. Consequently, we hypothesize that loss of ARID1a is an early step in transformation of endometriosis into OCCC. Here, we show that knocking down ARID1a in an immortalized endometriosis line, promotes greater invasion of basement membrane in vitro, and higher efficiency of anchorage-independent growth. Using two independent genome wide approaches to assay chromatin accessibility and DNA methylation, we demonstrate that the loss of ARID1a does not significantly alter global chromatin accessibility and DNA methylation with the exception of the genomic regions containing late replicating domains. Our findings do however indicate that the loss of ARID1a contributes to altered distribution of H3K27me3 and H3K27ac marks. Specifically we find an increased deposit of the polycomb repressive mark in the knock-down line outside of promoters. Interestingly, we also find the knock-down line has a higher level of the active mark H3K27ac at the promoters and a lower level at the enhancers relative to the scrambled control. Moreover, many of the genes differentially expressed upon ARID1a knock-down are consistent with the changes of H3K27ac at the respective gene promoter. We therefore conclude that loss of ARID1a expression contributes to cellular transformation through deregulation of gene expression primarily through alteration of histone marks.

Citation Format: Ranjani Lakshminarasimhan, Claudia Andreu-Vieyra, Kate Lawrenson, Simon A. Gayther, Peter A. Jones, Gangning Liang. The role of chromatin remodeler protein ARID1a in ovarian clear cell carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B02.
Abstract B03: Identification of epigenetic regulated genes through simultaneous analysis of DNA methylation and chromatin structure in uncultured tumors
Authors: Becket Elinne , Chopra Sameer , Duymich Christopher , Justin Lin J. , You Jueng Soo , Pandiyan Kurinji , Nichols Peter W. , Siegmund Kimberly D. , Jones Peter A. , Liang Gangning
Published: May 2016

The contribution of promoter DNA methylation to the alteration of caner related gene expression has been well studied, however, these genes can also potentially be altered by chromatin accessibility without involvement of DNA methylation and can be epigenetically inherited. In this study, we used an assay developed in our laboratory (AcceSssIble) that can simultaneously interrogate DNA methylation and chromatin accessibility allowing us to investigate the epigenetic changes in uncultured clear cell renal cell carcinoma (ccRCC) tumors and normal tissue to uncover genes that contribute to ccRCC tumorigenesis. AcceSssIble is both cost-effective and easily analyzed using simple and straightforward computational analysis. Our study revealed significant changes to the epigenome of ccRCC, especially identifying epigenetically up- (160) or down-regulated genes (180), which are dependent on accessibility changes with (30%) or without (70%) DNA methylation involvement, and which were validated by a cross-correlation of the identified genes with RNA-seq and DNA methylation data from larger cohorts of ccRCC samples from The Cancer Genome Atlas (TCGA). In addition, our findings also revealed these sets of genes not found to be commonly mutated in ccRCC and undergo epigenetic changes at higher frequencies than common ccRCC mutations. In addition, pathway analysis suggests that genetic and epigenetic alterations are independent events, and one such example includes a set of changes in HIF1α signaling pathway genes that are independent of the Von Hippel-Lindau (VHL) status. This suggests a novel epigenetic basis for HIF1αs role during tumorigenesis that may be a common occurrence in ccRCC. Thus, the AcceSssIble analysis on ccRCC samples revealed novel candidates for epigenetic driver genes which were previously undetectable by widely used methylation studies. Overall, this study provides a novel approach that can help identify new epigenetic therapeutic targets and treatment strategies complementing current approaches based primarily on the genetic makeup of primary tumors.

Citation Format: Elinne Becket, Sameer Chopra, Christopher Duymich, Lin J. Justin, Jueng Soo You, Kurinji Pandiyan, Peter W. Nichols, Kimberly D. Siegmund, Peter A. Jones, Gangning Liang. Identification of epigenetic regulated genes through simultaneous analysis of DNA methylation and chromatin structure in uncultured tumors. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B03.
Abstract B21: Integrated genomic and functional analyses of histone demethylases identify oncogenic KDM2A isoform in breast cancer
Authors: Yang Zeng-Quan
Published: May 2016

Histone lysine demethylases (KDMs) comprise a large class of enzymes that catalyze site-specific demethylation of lysine residues on histones and other proteins. They play critical roles in controlling transcription, chromatin architecture, and cellular differentiation. However, the genomic landscape and clinical significance of KDMs in breast cancer remain poorly characterized. Here, we conducted a meta-analysis of 24 KDMs in breast cancer and identified associations among recurrent copy number alterations, gene expression, breast cancer subtypes, and clinical outcome. Two KDMs, KDM2A and KDM5B, had the highest frequency of genetic amplification and overexpression. Furthermore, among the 24 KDM genes, KDM2A had the highest correlation between copy number and mRNA expression, and high mRNA levels of KDM2A were significantly associated with shorter survival of breast cancer patients. KDM2A has two isoforms: the long isoform is comprised of a JmjC domain, CXXC-zinc finger, PHD zinc finger, F-box, and the AMN1 protein domain; whereas the short isoform of KDM2A lacks the N-terminal JmjC domain but contains all other motifs. Detailed characterization of KDM2A in breast cancer revealed that the short isoform of KDM2A is more abundant than the long isoform at DNA, mRNA, and protein levels in a subset of breast cancers. Furthermore, our data indicate that the short isoform of KDM2A has oncogenic potential and functions as an oncogenic isoform in a subset of breast cancers. Taken together, our findings suggest that amplification and overexpression of the KDM2A short isoform is critical in breast cancer progression.

Citation Format: Zeng-Quan Yang. Integrated genomic and functional analyses of histone demethylases identify oncogenic KDM2A isoform in breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B21.
Abstract B30: Targeting EZH2 methyltransferase activity: A novel therapeutic approach to ARID1A-deficient cancer
Authors: Bitler Benjamin , Garipov Azat , Shih Ie Ming , Zhang Rugang
Published: May 2016

Loss of function mutation of the epigenetic modulator ARID1A, a component of SWI/SNF chromatin remodeling complex, occurs in a number of cancers most notably ovarian. ARID1A is mutated in up to 60% and 30% of clear cell and endometrioid ovarian cancers, respectively. However, there currently is no effective therapy that targets ARID1A-deficient human cancers. Here we show ARID1A-deficient ovarian cancer cells are selectively sensitive to inhibition of EZH2's methyltransferase activity. EZH2 is the catalytic subunit of the polycomb repressor complex 2, which represses gene expression by generating tri-methylation epigenetic mark on lysine 27 of histone H3 (H3K27Me3). Utilizing a library of small molecules against epigenetic targets, we identified an EZH2 small molecule inhibitor that selectively inhibited the growth of ARID1A-deficient ovarian cancer cells, while exhibiting no effects in ARID1A wild-type cells. Genome-wide gene expression profile revealed that there is significant overlap of genes altered by ARID1A restoration and EZH2 methyltransferase inhibition. Specifically, the tumor suppressor and inhibitor of PI3K/AKT signaling, PIK3IP1, is regulated by both ARID1A and EZH2. Chromatin immunoprecipitation assays confirmed the occupancy of ARID1A and EZH2 at the PIK3IP1 promoter. In an intraperitoneal (IP) xenograft mouse model, EZH2 inhibitor GSK126 treatment resulted in a significant decrease in the number of IP tumor nodules. Moreover, in an independent orthotopic intra-bursal xenograft model using ARID1A wildtype and deficient cells, the EZH2 inhibitor GSK126 only suppressed the growth of ARID1A-deficient tumors. Notably, the observed effects correlated with a decrease in expression of H3K27Me3, pAKT and Ki67, a cell proliferation marker, and an increase in PIK3IP1. These data indicate loss of ARID1A and gain of EZH2 could act in epigenetic concert to promote cancer phenotypes. Taken together, these findings imply that inhibition of the methyltransferase EZH2 represents a novel therapeutic strategy for ARID1A-deficient cancers.

Citation Format: Benjamin Bitler, Azat Garipov, Ie Ming Shih, Rugang Zhang. Targeting EZH2 methyltransferase activity: A novel therapeutic approach to ARID1A-deficient cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B30.
Abstract B49: Histone H3K27 tri-methylation regulates DPYD expression and cellular sensitivity of 5-fluorouracil
Authors: Wu Rentian , Offer Steven , Jerde Calvin , Dunlap Garrett , Diasio Robert
Published: May 2016

Dihydropyrimidine dehydrogenase (DPD) is a major determinant of the efficacy and toxicity of 5-fluorouracil in various cancer therapies. Single nucleotide polymorphisms (SNPs) within DPYD have been studied extensively for years. However, known SNPs do not explain most cases of altered DPD activity and response to 5-FU. Furthermore, variations of DPYD expression in cancer patients have been reported; however, the underlying molecular mechanism is unclear. This suggests that regulation of DPYD expression may be an additional mechanism to control DPD activity. In this study, we focused on epigenetic regulation of DPD and specifically investigated the role of histone methylation on DPYD expression. Inhibition of the H3K27 methyl-transferase Ezh2 by either GSK-126 or a dominant-negative histone H3 mutant significantly increased DPYD expression in various cell lines. The expression of thymidylate synthetase, a major target of 5-fluorouracil toxicity, was not altered. Consistent with elevated DPYD expression, cells that lost H3K27me3 were more resistant to 5-fluorouracil. Furthermore, we demonstrated that Ezh2 and H3K27me3 were enriched on the promoter and the first exon of DPYD in low-DPD expressing cells, but not in cell lines with high DPD levels. Additionally, the enrichment of H3K27me3 on the DPYD promoter was negatively correlated with cellular DPD activity in peripheral mononuclear cells from healthy volunteers. Finally, CRISPR/Cas9-mediated targeting of Ezh2 to the DPYD promoter artificially increased H3K27me3 and suppressed DPYD expression. Collectively, these data suggest that histone methylation can regulate DPYD expression, providing a previously unrecognized mechanism of 5-fluorouracil sensitivity. The tri-methylation of H3K27 is a potential biomarker for guiding individualized 5-FU therapy.

Citation Format: Rentian Wu, Steven Offer, Calvin Jerde, Garrett Dunlap, Robert Diasio. Histone H3K27 tri-methylation regulates DPYD expression and cellular sensitivity of 5-fluorouracil. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B49.
Abstract IA01: Epigenetic mechanisms of tumor initiation and evolution
Authors: Bernstein Bradley E.
Published: May 2016

The paramount importance of epigenetic regulation in cancer is now well established by a convergence of data from cancer genome sequencing, epigenomics and the transcriptional and molecular characterization of tumors and models. Our laboratory research is focused on characterizing epigenetic mechanisms of tumor initiation, as well as on understanding how epigenetic changes and intratumoral heterogeneity contribute to drug resistance and tumor relapse. We are particularly interested in brain tumors as clinically compelling models for investigating epigenetic mechanisms of tumorigenesis. I will present two ongoing projects in this area. The first project is focused on genetic mutations that affect epigenetic regulators and processes, and are associated with gliomagenesis. Here I will discuss our progress towards delineating specific mechanisms, regulatory targets and programs that explain the tumorigenicity of individual mutations. The second project is focused on epigenetic mechanisms that enable glioblastoma stem cells to adapt to environmental stressors or drug pressures. Here we have identified a specific role for histone demethylases in resetting the epigenetic landscapes of glioblastoma stem cells, and thereby allowing them to transition to a more primitive and refractory state. These respective studies exemplify ongoing research in our lab as well as in the broader research community, and have general relevance for cancer biology, diagnosis and therapy.

Citation Format: Bradley E. Bernstein. Epigenetic mechanisms of tumor initiation and evolution. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA01.
Abstract IA05: Genome-wide views into the mechanisms of transcription regulation
Authors: Lis John T. , Danko Charles , Duarte Fabiana , Mahat Dig Bijay
Published: May 2016

RNA Polymerase II (Pol II) is the molecular machine that transcribes all the protein-encoding mRNAs as well as a spectrum of non-coding regulatory RNAs. The distribution of Pol II reveals not only location and levels of transcription of these transcribed genes, but also, the distinctive patterns of divergent transcription that can be used to identify the active promoters and enhancers that regulate these genes. Moreover, by monitoring changes in the distribution of Pol II across genomes in response either to regulatory signals and to directed perturbations of transcription factors, the distinct steps in transcription that are regulated can be elucidated. With increasing positional and temporal resolution provided by new, genome-wide nuclear run-on and chromatin assays, we are able to gain critical insights into the mechanisms governing how polymerases initiate and elongate through transcription units, and into how these processes are regulated. In this presentation, I will provide a comprehensive genome-wide view of the rapid and dramatic changes in transcription that accompany the stress response, a long used model for studying regulation, and the factors and molecular mechanisms that regulate this reprogramed transcriptional response in both Drosophila and mammals.

Citation Format: John T. Lis, Charles Danko, Fabiana Duarte, Dig Bijay Mahat. Genome-wide views into the mechanisms of transcription regulation. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA05.
Abstract IA12: Long-range gene regulation in the context of chromatin domains
Authors: Dekker Job
Published: May 2016

The 3D organization of the genome is critical for gene regulation, genome stability and faithful transmission of chromosomes to daughter cells. We apply Chromosome Conformation Capture-based technologies to determine how cells fold their chromosomes and to discover the mechanisms that drive the spatial organization of genomes. I will discuss our recent proposal that in interphase nuclei mammalian chromosomes are hierarchically organized (Gibcus and Dekker, 2013). First, at the nuclear level, chromosomes are compartmentalized into large multi-Mb domains that are either active and open or inactive and closed. These compartments themselves are composed of smaller sub-Mb Topologically Associating domains (TADs) (Dixon et al. 2012, Nora et al. 2012). Finally, long-range gene regulation occurs within TADs through long-range looping interactions between genes and regulatory elements.

TAD organization and their role in gene regulation have important implications in cancer cells. I will highlight how genomic rearrangements in cancer genomes can lead to altered TAD organization and inappropriate gene expression, including increased expression of cancer promoting genes, and repression of cancer suppressing genes.

I will also highlight two new studies from my laboratory that reveal different roles of TADs in chromosome-wide gene regulation along the dosage compensated X-chromosomes. First, in C. elegans we find that a Condensin complex mediates TAD formation and dosage compensation. Second, in mouse the dosage compensated X chromosome folds in a unique way with global loss of TADs.

Citation Format: Job Dekker. Long-range gene regulation in the context of chromatin domains. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr IA12.
Abstract PR02: Transcriptional regulation mediated by biochemically distinct forms of SWI/SNF
Authors: Raab Jesse R. , Resnick Samuel , Magnuson Terry
Published: May 2016

Background: We often consider the SWI/SNF complex as a single entity with a single function in a particular cell type. This model ignores that multiple positions within the SWI/SNF chromatin remodeling complex can be filled by mutually exclusive subunits. Inclusion or exclusion of such subunits gives rise to an array of biochemically distinct chromatin remodeling complexes, some of which have profound functional consequences on gene regulation and differentiation. Here, we examine the functional relationships among three complex-specific ARID (AT-Rich Interacting Domain) subunits of the SWI/SNF complex in a human hepatocellular carcinoma cell line using ChIP-seq, RNA-seq, and public data on transcription factor binding.

Results: Using RNAi directed at each of the three subunits, we identify widespread overlap in transcriptional regulation mediated by SWI/SNF. The ARID subunits are commonly bound together at the promoters of active genes, with more variable binding associated with distal regulatory elements. ARID1B and ARID2 cooperate to repress the expression of hundreds of genes. Additionally, we identify many examples of competitive interactions between ARID1A and ARID1B or ARID2, and show that gene expression changes following loss of one ARID are dependent on the function of an alternative ARID. These distinct regulatory modalities are correlated with differential occupancy by transcription factors. Together these data suggest distinct SWI/SNF complexes dictate gene-specific transcription through interactions between different forms of SWI/SNF and specific co-factors. The ARID subunits are among the most frequently mutated chromatin regulators in cancer. Understanding the functional relationship between distinct forms of the complex is a necessary first step for identifying their potentially unique roles in oncogenesis.

Citation Format: Jesse R. Raab, Samuel Resnick, Terry Magnuson. Transcriptional regulation mediated by biochemically distinct forms of SWI/SNF. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr PR02.
Abstract B1-21: Network analysis implicates Panx3 as an adipocyte associated factor important during carcinogenesis
Authors: Halliwill Kyle D. , Quigley David , Chin Douglas , Le Phuong Thuy , Rosario Reyno Del , Balmain Allan
Published: May 2016

Recent studies exploring risk factors for cancer have unveiled a clear association between body mass index (BMI) and tumor development. However, the mechanistic details of this relationship remain obscure, in large part because of the complexity inherent to these two traits. In order to better understand this relationship, we have undertaken an investigation aimed at identifying genetic elements that influence both BMI and tumorigenesis in a carcinogen-driven mouse model of non-melanoma skin cancer. Using gene expression correlation network analysis we have identified a novel factor associated with both tumorigenesis and BMI, pannexin 3 (Panx3). Our investigation has placed Panx3 as a pivotal regulator of adipocyte signaling, with a clear association with tumorigenesis, suggesting it may play a major role in linking these phenotypes. Further research aimed at elucidating the role Panx3 plays during tumorigenesis, and how it influences adipocyte development and signaling, will be critical to our understanding of the relationship between these two traits.

Citation Format: Kyle D. Halliwill, David Quigley, Douglas Chin, Phuong Thuy Le, Reyno Del Rosario, Allan Balmain. Network analysis implicates Panx3 as an adipocyte associated factor important during carcinogenesis. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-21.
Abstract B1-53: Inhibiting stemness and invasion property of glioma stem cells by biguanide compound
Authors: Choi Junjeong , Lee Ji-Hyun , Shim Jin-Kyoung , Kim Pilnam , Kang Seok-Gu
Published: May 2016

Introduction: Ever since pharmacoepidemiologic clues of antineoplastic actions of metformin were reported in 2005, potential application of biguanide for the treatment of several types of cancer has been evaluated. To overcome limited pharmacokinetic properties of prototype biguanides such as metformin and penformin, a newly developed biguanide compound HL156A was developed. In the present, we assessed the potential biologic effect of HL156A on the glioma stemness and invasion properties. Methods: Using patient derived glioma cancer stem cells (gCSCs), we assessed cell viability, AMPK-mTOR pathway, stemness, differentiation, tumor invasion and epithelial-mesenchymal properties of gCSCs. In addition, expression profiles with drug treatment were obtained using Illumina HumanHT-12 v4 Expression BeadChip and gene set enrichment analysis (GSEA) was performed with GSEA application. Orthotopic tumor model was generated and assessed for tumor margin. Results: The compound activated p-AMPK and reduced phosphorylation of mTORC-1-regulated proteins. It decreased stemness of gCSCs, proved by sphere formation assay and decreased expression of stemness markers. The invasive properties of gCSCs were inhibited on 3D invasion assay and the expression of proteins related with epithelial-mesenchymal transition was inhibited by the compound. GSEA revealed cell adhesion related gene set was altered in the compound treated groups. Orthotopic model of the tumor showed less invasive tumor margin on the treatment of the compound.

Citation Format: Junjeong Choi, Ji-Hyun Lee, Jin-Kyoung Shim, Pilnam Kim, Seok-Gu Kang. Inhibiting stemness and invasion property of glioma stem cells by biguanide compound. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B1-53.
Abstract B2-08: Model order reduction for cell signaling pathways: An investigation of G-protein coupled receptor signaling
Authors: Talwai Prem M.
Published: May 2016

G-protein coupled receptors (GPCRs) are frequently overexpressed in human carcinomas, where they are responsible for stimulating the aberrant proliferation of cancer cells. Unfortunately, the mechanisms of this stimulation are poorly understood due to the complexity of the interactions between GPCRs and second-messenger pathways. Robust quantitative methods are therefore necessary to simplify mathematical models of GPCR-mediated signaling. Model order reduction aims to reduce the dimensionality of kinetic models of signaling pathways (such as the GPCR signal transduction system) in order to enable the computational investigation of complex signaling networks. Existing reduction procedures aim to eliminate “slaved species”, which have low net rates of formation. Unfortunately, these methods cannot be applied to reaction networks such as the GPCR system where receptor complexes exhibit high affinities for binding proteins (and therefore have low dissociation constants). This paper aims to develop a novel projection-based model reduction technique for reducing the dimensionality of kinetic models of cell signaling pathways (such as the GPCR signaling cascade). This algorithm (executed at the command-line interface) combines the techniques of proper orthogonal decomposition, trajectory piecewise linearization, and Krylov subspace reduction in an effort to identify a best-fit subspace for the model trajectories that accurately approximates the mapping between the model input and outputs. The command-line tool effectively reduced the dimensionality of a kinetic model of the GPCR network from 16 to 3. In addition, implementing the algorithm revealed strong correlations within two disjoint sets of participating species, suggesting the need to monitor the concentration of only one species from each set during a computational or experimental investigation. The model reduction procedure enables cell biologists to effectively employ kinetic models to analyze the mechanisms of uncontrolled cell proliferation. A comprehensive understanding of these mechanisms will aid pharmacologists in identifying therapeutic targets in cancer cells.

Citation Format: Prem M. Talwai. Model order reduction for cell signaling pathways: An investigation of G-protein coupled receptor signaling. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-08.
Abstract B2-12: A systems biology approach for the discovery of differentiation therapeutics
Authors: Li Yulin , Seita Jun , Felsher Dean , Dill David L.
Published: May 2016

Accurately assessing the changes in cellular differentiation status in response to drug treatments or genetic manipulations is crucial for understanding the tumorigenesis process and developing novel therapeutics for human cancer. Here we have developed a novel systems biology approach, called the Lineage Maturation Index (LMI), to define the changes in differentiation state of cancer cells based on their gene expression profiles. We have been focusing on hematopoietic malignancies, but this approach is applicable to many human cancer types. We define the expression profile of N genes within a cell to be a point in an N-dimensional space. A lineage vector is derived from a progenitor cell (such as a hematopoietic stem cell) to a mature cell (such as a granulocyte) based on the expression of these N genes. By projecting the expression profile of an unknown cell onto the lineage vector, an LMI can be computed for the differentiation state of this specific cell. Upon drug treatments or genetic manipulations, a shift in LMI from stem cells towards mature cell types indicates differentiation. We have confirmed that the LMI approach can track the differentiation of normal hematopoietic cells. We have further shown that differentiation is a major consequence of various targeted therapies against leukemia irrespective of the driving oncogenes. Most importantly, we have used this approach to analyze the Connectivity Map HL60 leukemia data set for drugs that can induce leukemia cells to differentiate. In addition to drugs known to have differentiation activities (such as all-trans retinoic acid and etoposide), we discovered that several novel drugs (such as dihydroergotamine, mebendazole, and clonidine) have potent differentiation activities in leukemia cells. Currently, we are expanding our study into multiple types of solid tumors, such as breast, prostate, and colon cancers. Our LMI approach is highly robust in characterizing differentiation of the cancer cells and discovering novel differentiation therapies for human cancer.

Citation Format: Yulin Li, Jun Seita, Dean Felsher, David L. Dill. A systems biology approach for the discovery of differentiation therapeutics. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-12.
Abstract B2-32: Networks dynamics and opposite effects of Wnt5a on motility in melanomas
Authors: Rasheed Mohammed , Bouaynaya Nidhal , Araysi Lita M. , Zhuo Tang , Li Mei , Zhou Ping , El-Kattan Kareem , Fathallah-Shaykh Hassan
Published: May 2016

Melanoma is an aggressive cancer whose incidence continues to rise worldwide; furthermore, metastatic melanoma is associated with poor prognosis. Wnt signaling may lead to conflicting effects on the biology of melanoma as it may either decrease or increase the incidence of metastasis. Here, we show that Wnt5a enhances motility in 3/5 cell lines and represses motility in the other two. We measured the effects of perturbations of the levels of Wnt5a, HADHB, Pirin, and Mart1 on the levels of the seven molecules, Wnt5a, HADHB, Pirin, Mart1, Ret1, Stc2, and S100B in the five cell lines. The results uncovered unanticipated nonlinear molecular dynamics. Seeking a mechanistic explanation, we built network models consisting of ordinary differential equations representing signed directed graphs of the interactions between the seven molecules in the five cell lines. Simulations validate the results of the perturbation experiments and reveal that the indirect network-mediated effects of a molecule on another may annul or reverse its direct effects. Furthermore, network analysis and biological validation link HADHB and Pirin to motility. In summary, the findings reveal: 1) opposite effects of Wnt5a on motility in melanomas, 2) HADHB and Pirin control motility through their effects on Wnt5a, and 3) molecular targeting yields nontrivial nonlinear molecular dynamics, which are not readily anticipated.

Citation Format: Mohammed Rasheed, Nidhal Bouaynaya, Lita M. Araysi, Tang Zhuo, Mei Li, Ping Zhou, Kareem El-Kattan, Hassan Fathallah-Shaykh. Networks dynamics and opposite effects of Wnt5a on motility in melanomas. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-32.