bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A01: Evaluation of H3K27me3 and EZH2 in pediatric glial and glioneuronal tumors shows decreased H3K27me3 in H3F3A K27M mutant GBM
Authors: Venneti Sriram , Garimella Mihir , Sullivan Lisa , Martinez Daniel , Huse Jason , Heguy Adriana , Santi Mariarita , Thompson Craig , Thompson Craig , Alexander Judkins 
Published: August 2014

Abstract
Histone H3F3A mutations are seen in ~30% of pediatric glioblastoma (GBMs) and involve either the lysine residue at position 27 (K27M) or glycine at position 34 (G34R/V). Sixteen genes encode histone H3, each variant differing in only a few amino acids. Therefore how mutations in a single H3 gene contribute to carcinogenesis is unknown. H3F3A K27M mutations are predicted to alter methylation of H3K27. H3K27me3 is a repressive mark critical to stem cell maintenance and is mediated by EZH2, a member of the polycomb-group (PcG) family. We evaluated H3K27me3 and EZH2 expression using immunohistochemistry in 76 pediatric brain tumors. H3K27me3 was lowered/absent in tumor cells but preserved in endothelial cells and infiltrating lymphocytes in 6/20 GBMs. H3K27me3 showed strong immunoreactivity in all other tumor subtypes. Sequencing of GBMs showed H3F3A K27M mutations in all 6 cases with lowered/absent H3K27me3. Further, these 6 GBMs with lowered/absent H3K27me3 in tumor cells showed a worse prognosis than GBMs with preserved H3K27me3. EZH2 expression was high in GBMs, but absent/focal in other tumors. However, no significant differences in EZH2 expression were observed between H3F3A K27M mutant and wild type GBMs, suggesting that EZH2 mediated trimethylation of H3K27 is inhibited in GBM harboring K27M mutations. Our results indicate that H3F3A K27M mutant GBMs show decreased H3K27me3 that may be of diagnostic, prognostic and biological relevance.
Citation Format: Sriram Venneti, Mihir Garimella, Lisa Sullivan, Daniel Martinez, Jason Huse, Adriana Heguy, Mariarita Santi, Craig Thompson, Craig Thompson, Judkins Alexander. Evaluation of H3K27me3 and EZH2 in pediatric glial and glioneuronal tumors shows decreased H3K27me3 in H3F3A K27M mutant GBM. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A01.
Abstract A23: Repression of Id4 (inhibitor of DNA binding 4) by the polycomb group protein EZH2 in prostate cancer
Authors: Chinaranagari Swathi , Sharma Pankaj , Chaudhary Jaideep 
Published: August 2014

Abstract
Introduction: Inhibitor of DNA binding/differentiation protein 4 (Id4) is dominant negative regulator of basic helix loop helix (bHLH) family of transcription factors. Id4 shares the homology of HLH domain with other Ids and lack the basic DNA binding region. Unlike Id1, Id2 and Id3, Id4 acts as a tumor suppressor in prostate cancer by attenuating cell proliferation and promote apoptosis. We have previously shown that decreased Id4 expression in prostate cancer is due to its promoter hypermethylation. In this study we investigated the molecular mechanism by which Id4 promoter is hypermethylated. Here, we demonstrate that Id4 promoter methylation is initiated by EZH2 dependent tri-methylation of histone 3 at lysine 27 (H3K27me3).
Experimental procedures: Id4 protein expression was analyzed on human prostate adenocarcinoma samples by Immunohistochemistry and prostate cancer cell lines (LNCaP, C81 and DU145) by Western blot. EZH2 was silenced in DU145 cells and confirmed through western blot and Immunocytochemistry. Chromatin Immunoprecipitation (ChIP) was performed with IgG, RNA polymerase, EZH2 and H3K27Me3 antibodies in both prostate cancer cell lines and prostate cancer tissue samples.
Results: IHC demonstrated decreased Id4 protein expression in human prostate tissue samples whereas higher nuclear Id4 expression was found in normal prostate tissues. Re-expression of Id4 in EZH2 silenced Du145 demonstrated that Id4 is regulated in an EZH2 dependent manner. ChIP data on prostate cancer samples and cell lines suggested EZH2 occupancy and H3K27Me3 marks in the Id4 promoter region in cell lines and prostate cancer tissue specimens.
Conclusions: Id4 appears as a potential tumor suppressor gene that is epigenetically silenced during prostate cancer development. H3K27Me3 marks and EZH2 occupancy suggest a PRC2 dependent mechanism in Id4 promoter silencing in prostate cancer.
Acknowledgement: The research was supported by NIH/NCI-RO1CA128914 and in part by NIH/NCRR/RCMI G12RR03062
Citation Format: Swathi Chinaranagari, Pankaj Sharma, Jaideep Chaudhary. Repression of Id4 (inhibitor of DNA binding 4) by the polycomb group protein EZH2 in prostate cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A23.
Abstract A25: Yin Yang 1 promotes AKT activation through direct protein binding
Authors: Zhang Qiang , Wan Meimei , Horita David A. , Miller Lance D. , Kridel Steven J. , Kute Timothy E. , Kulik George , Sui Guangchao 
Published: August 2014

Abstract
As a polycomb group protein, Yin Yang 1 (YY1) plays an important role in cancer epigenetics. YY1 regulates both gene expression and protein modifications, including histone acetylation and methylation. We recently reported a proliferative role of YY1 and its cytoplasmic presence in breast cancer. In the current study, we demonstrated that YY1 promotes AKT phosphorylation at S473, a marker of AKT activation. The immunostaining signal of YY1 and AKT(S473) phosphorylation positively correlated and colocalized in breast cancer tissues and cells. The oncogene protein binding (OPB) domain (G201-S226) of YY1 bound to AKT and was necessary for YY1 in promoting AKT phosphorylation. This novel function of YY1 is independent of its transcriptional activity because YY1 promoted AKT phosphorylation in an in vitro setting using purified proteins and YY1 mutants deficient in binding to DNA retained this activity. Our further studies revealed that YY1 interacted with the PH domain of AKT where PIP3 binds and its role in promoting AKT phosphorylation was abolished when we depleted mSIN1, a specific component of mTORC2 that mediates AKT(S473) phosphorylation. Thus, we discovered a PI3K-independent mechanism of mTORC2-mediated AKT activation stimulated by YY1 binding to its PH domain, which supports the proliferative role of YY1 in mammary oncogenesis.
Citation Format: Qiang Zhang, Meimei Wan, David A. Horita, Lance D. Miller, Steven J. Kridel, Timothy E. Kute, George Kulik, Guangchao Sui. Yin Yang 1 promotes AKT activation through direct protein binding. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A25.
Abstract A27: Altered epigenetic regulation of homeobox genes in human oral squamous cell carcinoma cells
Authors: Marcinkiewicz Katarzyna M. , Gudas Lorraine J. 
Published: August 2014

Abstract
It is estimated that 41,380 new patients will be diagnosed with cancer of the oral cavity and the pharynx and 7,890 will die of those diseases in 2013 in the United States alone. More than 90% of all oral cavity cancers are of the squamous cell carcinoma (SCC) type. We identified numerous homeobox genes as differentially expressed between non tumorigenic oral keratinocytes OKF6-TERT1R and tumorigenic SCC9 cells. Data from Oncomine, a cancer microarray database, suggest that homeobox (HOX) genes are also dysregulated in oral SCC patients. The activities of Polycomb repressive complexes (PRC), which cause epigenetic modifications, and retinoic acid (RA) signaling can control HOX gene transcription in stem cells. HOXB7, HOXC10, HOXC13, and HOXD8 transcripts are higher in SCC9 than in OKF6-TERT1R cells; using ChIP (chromatin immunoprecipitation) we detected the PRC2 protein SUZ12 and the epigenetic H3K27me3 mark on histone H3 at these genes in OKF6-TERT1R, but not in SCC9 cells. In contrast, IRX1, IRX4, SIX2, and TSHZ3 transcripts are lower in SCC9 than in OKF6-TERT1R cells. We detected SUZ12 and the H3K27me3 mark at these genes in SCC9, but not in OKF6-TERT1R cells. SUZ12 and H3K27me3 levels were not altered by RA at these HOX genes in SCC9 and OKF6-TERT1R cells. We conclude that altered activity of PRC2 is associated with dysregulation of homeobox gene expression in human SCC cells, and that this dysregulation potentially plays a role in the neoplastic transformation of oral keratinocytes. An exciting future direction would be the elucidation of the molecular mechanisms driving aberrant homeobox gene expression in transformed oral keratinocytes by assessing additional epigenetic histone and DNA modifications present at these genes. Such experiments are currently underway.
Citation Format: Katarzyna M. Marcinkiewicz, Lorraine J. Gudas. Altered epigenetic regulation of homeobox genes in human oral squamous cell carcinoma cells. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A27.
Abstract A47: Investigating Zbtb protein recognition of epigenetically modified DNA
Authors: Terooatea Tommy W. , Pandya Maya J. , Chugg Alan C. , Buck-Koehntop Bethany A. 
Published: August 2014

Abstract
Methylation of CpG dinucleotides is essential for genomic stability, control of gene expression and the regulation of chromatin structure in normal eukaryotic cells. Aberrant alterations in these genomic methylation patterns have been linked with many diseases, including cancer. This correlation has prompted the need to better understand the regulatory mechanisms of DNA methylation in gene transcription. The Zbtb family, consisting of Zbtb33, Zbtb4 and Zbtb38, is a set of methyl-CpG binding proteins (MBPs), which recognize both methylated as well as sequence-specific non-methylated DNA sites through conserved Cys2His2 zinc fingers. DNA recognition subsequently recruits chromatin remodeling machinery to the target site resulting in chromatin compaction and gene silencing. While sufficient evidence suggests that the Zbtb proteins play a role in cancer, an extensive analysis of the gene targets and signaling pathways regulated by each protein has yet to be investigated. Here we utilize an interdisciplinary approach combining cellular biology, molecular biology and structural biology to determine the epigenetic targets regulated by the Zbtb MBPs and to identify the protein region(s) necessary for high-affinity DNA recognition. Utilizing western blot analysis, we have determined that the three Zbtb proteins exhibit differential endogenous expression levels in a variety of cancer cell lines. Further, ChIP qRT-PCR analysis demonstrated that the occupancy of Zbtb33 at various methylated and sequence-specific genes was highly variable between the different cancer cell lines. Combined, these results suggest that the Zbtb proteins likely mediate differential signaling pathways in different cancers, possibly by targeting specific regulatory gene elements. Mapping of the global gene occupation for Zbtb33 in various cancer cell lines is in progress. Additionally, we have designed multiple protein constructs around the conserved Cys2His2 zinc finger DNA binding region as well as additional zinc fingers located in the C-terminal regions of Zbtb4 and Zbtb38, as the functions of the latter have not yet been identified. The constructs have been analyzed by solution NMR and EMSA to determine whether they are amenable for further structural analysis and to characterize their DNA binding interactions. This multidisciplinary approach provides the means for advancing our understanding of the molecular basis by which these proteins interpret and translate epigenetic signals in the cancerous state.
Citation Format: Tommy W. Terooatea, Maya J. Pandya, Alan C. Chugg, Bethany A. Buck-Koehntop. Investigating Zbtb protein recognition of epigenetically modified DNA. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A47.
Abstract B03: Loss of the Polycomb mark at bivalent promoters leads to activation of intestinal stem cell genes in colorectal cancer
Authors: Hahn Maria A. , Li Arthur X. , Wu Xiwei , Rosenberg Daniel W. , Pfeifer Gerd P. 
Published: August 2014

Abstract
During tumor formation, transcription of many genes becomes deregulated. In order to elucidate epigenetic mechanisms responsible for this phenomenon, we analyzed genome-wide patterns of several histone marks, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in human stage II colorectal cancer and matching normal tissue samples. By using liquid chromatography—mass spectrometry (LC-MS/MS), we determined that colon tumors have strongly reduced global levels of 5hmC. However, Tet-assisted bisulfite sequencing showed that site-specific loss of 5hmC in tumors is not associated with localized aberrant CpG island hypermethylation. We observed that DNA hypermethylation is generally targeted to bivalent promoters, which loose H3K27me3 and the associated genes are repressed effectively. Importantly, loss of H3K27me3 at bivalent promoters is not always coupled with gain of 5mC. Instead, H3K27me3 loss is also frequently associated with activation of intestinal stem cell markers and stem cell regulators including LGR5, SOX9, CDX1, CDX2, KLF5, and SALL4 as well as activation of many genes linked to colorectal cancer progression such as MET, CLDN1, PTGS2 (COX-2) and CCND1 (cyclin D1). Activation of these genes correlates with accumulation of the active chromatin mark H3K4me3 at their promoters. Our study demonstrates two distinct features of H3K27me3 loss in cancer. Loss of H3K27me3 at bivalent genes can be accompanied by either gain of 5mC and strong repression or by persistence or gain of H3K4me3 and gene activation. We propose that instability of H3K27me3 coupled with selection for tumor-promoting events plays a major role in colorectal cancer progression most notably by causing activation of cancer driving genes including factors involved in stem cell maintenance.
Citation Format: Maria A. Hahn, Arthur X. Li, Xiwei Wu, Daniel W. Rosenberg, Gerd P. Pfeifer. Loss of the Polycomb mark at bivalent promoters leads to activation of intestinal stem cell genes in colorectal cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B03.
Abstract B18: Western diet-fed mice with inherited cancer predisposition reveal early epigenetic changes and protein markers for colon oncogenesis
Authors: Bebek Denis Dermadi , Valo Satu , Pussila Marjaana , Reyhani Nima , Sarantaus Laura , Nystrom Minna 
Published: August 2014

Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related deaths in the Western world. Interactions between genetic and environmental factors, such as diet, are suggested to play a critical role in its etiology. However, the mechanisms that mediate the effects of diet on oncogenesis are largely unknown. We conducted a long-term feeding experiment in the mouse to address epigenetic changes arising in normal colonic mucosa and their functional consequences as putative cancer-predisposing events available for early detection.
The quantitative analysis of proteomes and the expression of 94 growth-regulatory genes previously linked to human CRC and aberrant hypermethylation were studied at two time points (5 weeks and 12 months of age) in the heterozygote Mlh1+/- mice analogous to human Lynch syndrome, and wild type Mlh1+/+ littermates, fed with Western-style (WD) or AIN-93G control diet. In the proteome study the most significant expression changes were found in the Mlh1+/- WD mice compared to mice fed with AIN-93G control diet and the 19 identified proteins mainly point to abnormities in energy metabolism and protein unfolding. We further found that in mice carrying Mlh1 mutation and/or fed with WD, histologically normal proximal colonic mucosa exhibited a significant expression decrease in tumor suppressor genes, Dkk1, Slc5a8, Hoxd1, and Socs1. Especially in Dkk1, a secreted antagonist of the Wnt/β-catenin pathway the reduced expression was associated with its promoter hypermethylation. The fact that changes in Dkk1 seem to predispose to neoplasia in the proximal colon and that 5 out of 6 mice with neoplastic colonic lesions were fed with WD suggests that the found expression changes are early markers for oncogenesis.
Citation Format: Denis Dermadi Bebek, Satu Valo, Marjaana Pussila, Nima Reyhani, Laura Sarantaus, Minna Nystrom. Western diet-fed mice with inherited cancer predisposition reveal early epigenetic changes and protein markers for colon oncogenesis. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B18.
Abstract B41: Methylome profiling identifies unique patterns of DNA methylation in endometrial cancers
Authors: Trimarchi Michael P. , Yan Pearlly S. , Huang Kun , Groden Joanna , Bundschuh Ralf , Goodfellow Paul J. 
Published: August 2014

Abstract
Introduction: DNA methylation is a stable epigenetic mark often perturbed during carcinogenesis. Growing evidence demonstrates a role for DNA methylation both as a regulator of gene expression and as a potential biomarker. Widespread accumulation of methylation in regulatory elements in certain cancers (termed the CpG island methylator phenotype) may play a role in carcinogenesis. Few studies, however, have investigated genome-wide methylation in a clinical cohort, as the methodology for analyzing these large datasets remains poorly developed. Endometrial cancer is the most common female gynecological cancer in the US, with sporadic endometrioid as the predominant subtype.
Methods: This study profiles the methylomes of 76 sporadic endometrioid endometrial primary tumors and 12 normal endometrium using sequenced methylated fragments captured by the MBD protein (MethylCap-seq).
Results: Analysis of bulk methylation in promoter CpG islands (CGI) identified a subset of tumors with a putative methylator phenotype. We are currently developing a gene signature to more easily detect endometrial tumors with a methylator phenotype, perform cross-platform analyses, and further characterize clinicopathological variables associated with the phenotype. We have also developed a pipeline for quality analysis and show that exclusion of poor quality samples increases statistical power to call differential methylation and reduces analysis artifacts.
Conclusion: The results of our study highlight MethylCap-seq as a useful tool for profiling methylation patterns in large clinical datasets.
Citation Format: Michael P. Trimarchi, Pearlly S. Yan, Kun Huang, Joanna Groden, Ralf Bundschuh, Paul J. Goodfellow. Methylome profiling identifies unique patterns of DNA methylation in endometrial cancers. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B41.
Abstract B48: Targeting SETD2 knockout cells: A synthetic lethal approach to treating ccRCC
Authors: Fahey Catherine C. , Hacker Kathryn E. , Jin Jian , Davis Ian J. , Rathmell W. Kimryn 
Published: August 2014

Abstract
Background: Kidney cancer is estimated to affect 65,150 newly diagnosed individuals in 2013. Approximately 70% of these diagnoses will be clear cell renal cell carcinoma (ccRCC). Many targeted therapies for ccRCC are currently being pursued, as ccRCC is resistant to radiation and often does not respond to chemotherapy. The most commonly mutated tumor suppressor gene in ccRCC is VHL, located on chromosome 3. The loss of chromosome 3p is a high frequency event in ccRCC, which often also encompasses the genes PBRM1, BAP1, and SETD2. Mutations in one or more of these genes represent the next most common common genetic alterations in ccRCC. In our preliminary data, we have observed that mutations in SETD2, in particular, area associated with global deficits in chromatin packaging and organization.
Methods: We are pursuing the opportunity to exploit SETD2 loss as a source of cellular fragility by performing a small molecule screen on SETD2 wild type and SETD2 knockout cell lines. We will use a screening set of epigenetically targeted compounds to perform a high throughput screen with cell viability as the endpoint, as well as use a selected few compounds to compare effect on wild type and knockout cells in a more in depth manner.
Results: Preliminarily, we have tested SETD2 knock-down lines to confirm that we can effectively preform all aspects of this screen. In our current studies, we are repeating testing with the selected few compounds and beginning the high throughput screen with a SETD2 knockout cell line.
Conclusion: Mutations in chromatin modifying genes in ccRCC present an opportunity for synthetic therapeutic approaches to induce reduced cell viability, as well as to identify unique meaningful interactions between chromatin modifier genes.
Citation Format: Catherine C. Fahey, Kathryn E. Hacker, Jian Jin, Ian J. Davis, W. Kimryn Rathmell. Targeting SETD2 knockout cells: A synthetic lethal approach to treating ccRCC. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B48.
Abstract B50: Selectively targeting prostate cancer with antiandrogen-equipped histone deacetylase inhibitors
Authors: Gryder Berkley E. , Akbashev Michelle J. , Rood Michael K. , Dillard Paulette , Khan Shafiq , Oyelere Adegboyega K. 
Published: August 2014

Abstract
Diverse cellular processes relevant to cancer progression are regulated by the acetylation status of proteins, such as chromatin remodeling via histone proteins, controlled by opposing histone deacetylase (HDAC) and histone acetyltransferase (HAT) enzymes. Histone deacetylase inhibitors (HDACi) show great promise in preclinical cancer models, but clinical trials for solid tumors have failed to improve patient survival. This is due in part to an inability of HDACi to effectively accumulate in cancerous cells. To address this problem we designed HDACi with secondary pharmacophores to facilitate selective enrichment in malignant cells. We present the first example of HDACi compounds targeted to prostate tumors by equipping them (via “click” chemistry) with the secondary ability to bind the androgen receptor (AR) with non-steroidal antiandrogen moieties. Leads among these new duel-acting molecules bind to the AR and halt AR transcriptional activity at lower concentrations than clinical antiandrogens. They inhibit key isoforms of HDAC with improved potency over clinically approved HDACi, SAHA. Fluorescent microscopy reveals varying degrees of AR nuclear localization in response to these compounds. These biological properties translate into anticancer activity against hormone independent (AR-) DU145 prostate cancer, and even more so against hormone dependent (AR+) LNCaP, while having greatly reduced toxicity in non-cancerous cells. These compounds illustrate a “smart bomb” approach towards achieving selective, safe, and potent cancer therapies.
Citation Format: Berkley E. Gryder, Michelle J. Akbashev, Michael K. Rood, Paulette Dillard, Shafiq Khan, Adegboyega K. Oyelere. Selectively targeting prostate cancer with antiandrogen-equipped histone deacetylase inhibitors. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B50.