bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B28: Investigation of MGMT methylation patterns in diffuse large B-cell lymphoma using a novel allelic methylation-specific PCR pyrosequencing assay
Authors: Kristensen Lasse Sommer , Treppendahl Marianne Bach , Girkov Mia Seremet , Asmar Fazila , Nielsen Helene Myrtue , Kjeldsen Tina , Ralfkiaer Elisabeth , Hansen Lise Lotte , Grønbæk Kirsten 
Published: August 2014

Abstract
MGMT is a tumor suppressor gene, which becomes methylated in many different cancers including diffuse large B-cell lymphoma (DLBCL). Methylation of MGMT has been associated with the T-allele of the rs16906252 SNP found in the MGMT promoter. However, allelic MGMT methylation patterns and a possible association with the T-allele of this SNP have not been investigated in DLBCL. Today, standard treatment for DLBCL patients is rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP), and methylation of MGMT has been shown to predict chemosensitivity to the alkylating agent cyclophosphamide in the era before rituximab. We developed a novel method for the analysis of allelic MGMT methylation patterns based on pyrosequencing of antisense methylation specific PCR (MSP) products including the rs16906252 SNP. Samples from 148 DLBCL patients, of which 75 received R-CHOP, were studied using this assay. Standard bisulfite pyrosequencing and bisulfite sequencing of single clones were used to confirm data obtained by allelic MSP pyrosequencing. The allelic MSP pyrosequencing assay could reliably analyze allelic methylation patterns in standards of known allelic methylation status even when diluted in unmethylated DNA down to 1.25% methylation. MGMT methylation was observed for 28 patients of which seven were heterozygous. Thus, an association between the T-allele and MGMT methylation was observed (p-value =0.04). Among the seven methylated and heterozygous patients, two were methylated at both alleles, four were methylated only at the T-allele, and one only at the C-allele. Finally, we found no statistical significant associations between MGMT methylation or SNP genotypes with clinical parameters among the R-CHOP treated patients. In conclusion, allelic MSP pyrosequencing is a fast and cost-efficient method for evaluation of allelic methylation patterns, which may have wide implications for locus specific methylation analysis of tumor suppressor genes in future cancer research.
Citation Format: Lasse Sommer Kristensen, Marianne Bach Treppendahl, Mia Seremet Girkov, Fazila Asmar, Helene Myrtue Nielsen, Tina Kjeldsen, Elisabeth Ralfkiaer, Lise Lotte Hansen, Kirsten Grønbæk. Investigation of MGMT methylation patterns in diffuse large B-cell lymphoma using a novel allelic methylation-specific PCR pyrosequencing assay. [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 B28.
Abstract B38: Epigenetic effects of viral proteins on global levels of 5-hydroxymethylcytosine in HBV- and HCV-associated hepatocellular carcinoma in mice
Authors: Jiang Yong , Nie Ting , Kohler James , Bassit Leda , Goldenberg Daniel , Feitelson Mark , Schinazi Raymond F. 
Published: August 2014

Abstract
Hepatitis B virus (HBV) and hepatitis C virus (HCV) have both distinct and shared pathways to mediate development of virus-associated hepatocellular carcinoma (HCC). It has been postulated that viral encoded proteins such as HCV polyprotein or HBV X protein (HBx) induce epigenetic changes that can lead to HCC during chronic infection. 5-Hydroxymethylcytosine (5hmC) is a recently identified cytosine variant and an intermediate in enzyme-catalyzed active DNA demethylation. 5hmC is also considered a stable epigenetic mark during embryo development and tumorigenesis. Herein, we developed a liquid chromatography-mass spectrometry (LC-MS) based approach to assess global genomic 5hmC levels in tissues using several transgenic (Tg) mouse models to determine epigenetic changes induced by HBV and HCV viral proteins and role in pathogenesis of HCC.
A 2-to 3-fold reduction in genomic 5hmC was observed in liver samples from both Mdr2-knockout (Mdr2-KO) mice (a model of chronic inflammation-mediated HCC) and Mdr2-KO/HCV-Tg mice (a model carrying Mdr2-KO and HCV polyprotein). Interestingly, a similar fold reduction in 5hmC was detected in (Mdr2+/-)/HCV-Tg mice, which express HCV polyprotein, but do not develop HCC. In parallel, 5hmC levels were assessed in HBx-Tg mice with high-frequency of HCC. However, reduction of 5hmC was not detectable in liver samples from HBx-Tg mice as late as 14 months of age.
These results suggest that HCV polyprotein may accelerate inflammation-associated hepato-carcinogenesis in the Mdr2-KO/HCV-Tg mice. Therefore, we speculate that the HCV proteins may directly induce deconstruction of genomic 5hmC to promote HCC development. In contrast, our results in HBx-Tg mice suggest that HBx may employ a different epigenetic mechanism on 5hmC from that of HCV polyprotein. Notably, a significant change in genomic 5hmC was observed early at the pre-cancerous stages of HCC development in Mdr2-KO mice. This finding implies that, during chronic inflammation, a precipitous drop in 5hmC emerges prior to tumor formation. Therefore, 5hmC may provide an important diagnostic marker for early detection of HCC in persons with HCV chronic infection.
Citation Format: Yong Jiang, Ting Nie, James Kohler, Leda Bassit, Daniel Goldenberg, Mark Feitelson, Raymond F. Schinazi. Epigenetic effects of viral proteins on global levels of 5-hydroxymethylcytosine in HBV- and HCV-associated hepatocellular carcinoma in mice. [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 B38.
Abstract B57: Non-peptide macrocyclic histone deacetylase inhibitors: A structure activity relationship study
Authors: Tapadar Subhasish , Raji Idris , Fathi Shaghayegh , Mwakwari Celinah , Raftery Eric , Oyelere Adegboyega K. 
Published: August 2014

Abstract
Histone deacetylase (HDAC) inhibition is a promising therapeutic strategy for cancer treatment because HDAC inhibitors have shown the ability to arrest proliferation of nearly all transformed cell lines. Recently, we have reported a new class of hydroxamic acid based HDAC inhibitors containing 14- or 15-membered non-peptide macrolide antibiotic (azithromycin, clarithromycin, and TE-802) skeletons as surface recognition group. In these HDAC inhibitors, the modified macrolide antibiotic is linked to the zinc chelating hydroxamic acid moiety via 5- or 6-methylene chain linker. All the compounds showed low nano-molar HDAC inhibitory activities and they selectively inhibited the growth of both small cell and non-small cell lung cancer cells over the healthy cells at concentrations more than 5 times the IC50 values. Azithromycin-linked hydroxamic acids selectively accumulate in vivo in the lung tissues of Bald/C mice, allowing for tissue targeted anti-cancer therapy. To further understand the depth of the SAR of this class of HDAC inhibitors on HDAC inhibitory activities and HDAC isoform selectivity, we investigated the consequence of incorporation of varied methylene-linkers, newly modified macrolide antibiotic skeleton, and new macrocyclic skeleton. We observed that these compounds retain anti-HDAC, anti-proliferative activities and in some cases therapeutic profile is even better than previously reported compounds.
Citation Format: Subhasish Tapadar, Idris Raji, Shaghayegh Fathi, Celinah Mwakwari, Eric Raftery, Adegboyega K. Oyelere. Non-peptide macrocyclic histone deacetylase inhibitors: A structure activity relationship study. [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 B57.
Abstract B63: MBD3 accumulates at promoters and enhancers of active genes
Authors: Shimbo Takashi , Du Ying , Grimm Sara , Dhasarathy Archana , Mav Deepak , Shah Ruchir , Shi Huidong , Wade Paul A. 
Published: August 2014

Abstract
The Mi-2/nucleosome remodeling and histone deacetylase (NuRD) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities. Recent reports describing localization of NuRD are not in complete agreement and provide new insights that question previous models on NuRD action. Here, we provide location analysis of endogenous MBD3, a component of NuRD complex, in two human breast cancer cell lines (MCF7 and MDA-MB-231) using two independent genomic techniques: DNA adenine methyltransferase identification (DamID) and ChIP-Seq. Contrary to existing models, MBD3 preferentially associated with CpG rich promoters marked by H3K4me3 and lacking 5-methyl C or 5-hydroxymethyl C. MBD3 also showed cell-type specific localization across gene bodies, peaking around the transcription start site (TSS). A subset of sites bound by MBD3 was enriched in H3K27Ac and was in physical proximity to promoters in three dimensional space, suggesting function as enhancers. MBD3 enrichment was also noted at promoters modified by H3K27me3. These data suggest that MBD3, and by extension the Mi-2/NuRD complex, may have multiple roles in fine tuning expression for both active and silent genes. These data represent an important step in defining regulatory mechanisms by which Mi-2/NuRD complex controls chromatin structure and modification status.
Citation Format: Takashi Shimbo, Ying Du, Sara Grimm, Archana Dhasarathy, Deepak Mav, Ruchir Shah, Huidong Shi, Paul A. Wade. MBD3 accumulates at promoters and enhancers of active genes. [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 B63.
Abstract IA09: Nucleotide biosynthetic enzyme GMP Synthase is a relay of p53 stabilization in response to genomic stress
Authors: Verrijzer Peter 
Published: August 2014

Abstract
Nucleotide biosynthesis is fundamental to normal cell proliferation and to oncogenesis. An adequate nucleotide supply is crucial to support accurate DNA replication, DNA repair and transcription. The metabolism of cancer cells is characterized by elevated rates of de novo nucleotide biosynthesis that fuel rapid cycles of cell growth and division. Here we will discuss the role of the nucleotide biosynthetic enzyme guanosine 5′-monophosphate synthase (GMPS) in regulation of the p53 tumor suppressor pathway. In addition to its essential biosynthetic function, GMPS associates with the ubiquitin-specific protease 7 (USP7). Biochemical and genetic evidence established that GMPS is required for histone H2B deubiquitylation by USP7 in Drosophila and human cells. GMPS-USP7 is targeted to specific genomic loci to direct gene expression. For example, GMPS-USP7 enhances Polycomb-directed silencing of homeotic genes. We found that GMPS is also a crucial relay of p53 tumor suppressor stabilization, in response to genomic stress. Nuclear GMPS drives the transfer of MDM2-bound p53 to a GMPS-USP7-p53 deubiquitylation complex. GMPS is crucial for the deubiquitylation and stabilization of p53 by USP7. Normally, GMPS is sequestered in the cytoplasm, separate from the nuclear USP7 and p53. Genomic stress triggers the accumulation of GMPS in the nucleus, where it can stimulate p53 stabilization by USP7. Our results suggest that GMPS, a classic biosynthetic enzyme that enables cell growth and DNA replication, is also a crucial relay of cell proliferation restriction by p53. We suspect that the connection between nucleotide biosynthetic enzymes and transcription control might be important for the cellular defense against genomic instability or replicative stress involving deficiencies in the nucleotide pool. These findings show that cellular processes that are commonly assumed to involve separate molecular machineries can be surprisingly intimately connected.
Citation Format: Peter Verrijzer. Nucleotide biosynthetic enzyme GMP Synthase is a relay of p53 stabilization in response to genomic stress. [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 IA09.
Abstract IA10: Mechanisms regulating polycomb group proteins to target genes
Authors: Wu Xudong , Riising Eva M. , Comet Itys , Helin Kristian 
Published: August 2014

Abstract
The Polycomb group (PcG) proteins have attracted a lot of attention, because of their documented role in regulating cellular identity and differentiation. Moreover, the expression of the proteins is frequently deregulated in human cancer, and the PcG proteins are therefore considered attractive targets for anti-cancer therapy. The PcGs generally form multi-subunit chromatin-modifying complexes to maintain transcriptional repression in multicellular organisms. However, the mechanisms leading to the recruitment of PcG proteins to target genes are still not completely understood. At the meeting, some of our recent findings understanding the mechanisms that regulate the binding of PcG proteins to target genes and how they contribute to transcriptional regulation will be presented.
Citation Format: Xudong Wu, Eva M. Riising, Itys Comet, Kristian Helin. Mechanisms regulating polycomb group proteins to target genes. [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 IA10.
Abstract IA23: Functional and structural studies of HP1 heterochromatin
Authors: Canzio Daniele , Liang Moafu , Naber Nariman , Larson Adam , Marina Diana , Garcia Jennifer , Madhani Hiten , Cooke Roger , Schuck Peter , Cheng Yifan , Narlikar Geeta J. 
Published: August 2014

Abstract
During normal development the spread of heterochromatin provides a mechanism to heritably silence large regions of the genome. This allows selective transcription of a subset of genes required for determining and maintaining cell identity. Defects in heterochromatin assembly are associated with various cancers including breast cancer metastasis and acute myeloid leukemias. The most conserved form of heterochromatin is characterized by methylation of lysine 9 on histone H3 (H3K9me3). Key to both the assembly and the spreading process is the heterochromatin protein 1 (HP1), which binds the H3K9me3 mark via its chromodomain (CD). This interaction forms a versatile platform for recruitment of diverse chromatin modifying proteins. However, the molecular basis of how the HP1-H3K9me3 chromatin complex achieves these diverse interactions is poorly understood. Our work on the major S. pombe HP1 protein, Swi6, suggests that Swi6 switches between an auto-inhibited state and a spreading competent state upon binding methylated chromatin. Cryo-EM allows visualization of the spreading competent state of Swi6 on a methylated nucleosome. Our data suggest testable hypothesis for how specific post-translation modifications on HP1 can regulate its association with methylated chromatin and its interaction with different heterochromatin proteins.
Citation Format: Daniele Canzio, Moafu Liang, Nariman Naber, Adam Larson, Diana Marina, Jennifer Garcia, Hiten Madhani, Roger Cooke, Peter Schuck, Yifan Cheng, Geeta J. Narlikar. Functional and structural studies of HP1 heterochromatin. [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 IA23.
Abstract PR01: Global chromatin profiling identifies NSD2 mutations in pediatric acute lymphoblastic leukemia
Authors: Jaffe Jacob , Wang Yan , Chan HoMan , Zhang Jinghui , Huether Roberts , Kryukov Gregory , Taylor Jordan , Hu Min , Englund Nathan , Yan Feng , Wang Zhaofu , Wei Lei , Wei Lei , Ma Jing , Easton John , Sellers William R. , Keen Nicholas , Liu Jun , Liu Jun , Mullighan Charles , Carr Steven , Downing James , Garraway Levi , Stegmeier Frank 
Published: August 2014

Abstract
Epigenetic dysregulation is an emerging hallmark of cancers, and the identification of recurrent somatic mutations in chromatin modifying enzymes implies a causal role for altered chromatin states in tumorigenesis. While the genomic characterization of cancers is well advanced, our current understanding of cancer epigenomes is limited. Here, we developed a high-information-content mass spectrometry approach to profile global histone modifications in human cancer cells. When applied to 115 cell lines of the Cancer Cell Line Encyclopedia, this approach identified distinct molecular chromatin signatures (MCS) that provided novel insights into their epigenetic states. One MCS cluster, characterized by high H3K27 trimethylation, strongly correlated with EZH2 gain-of-function mutations, whereas another MCS cluster provided functional epigenetic correlates of EZH2 loss-of-function mutations. A third MCS cluster was characterized by increased H3K36 dimethylation and contained several cell lines harboring NSD2 translocations. Analysis of genomic correlates of the remaining cell lines within this third cluster identified a novel NSD2 E1099K variant in acute lymphoblastic leukemia (ALL) lines. Ectopic expression of the NSD2 E1099K variant induced a MCS profile characteristic of NSD2 hyperactivation and promoted transformation. Moreover, NSD2 knockdown selectively inhibited the proliferation of cell lines harboring NSD2 mutations. Massively parallel sequencing analysis of over 1000 pediatric cancer genomes identified the same NSD2 E1099K mutation in 14% of t(12;21)[ETV6-RUNX1]-containing ALLs. Together, these findings identify NSD2 as a potential therapeutic target for pediatric ALL and provide a general framework for the functional annotation of cancer epigenomes.
Citation Format: Jacob Jaffe, Yan Wang, HoMan Chan, Jinghui Zhang, Roberts Huether, Gregory Kryukov, Jordan Taylor, Min Hu, Nathan Englund, Feng Yan, Zhaofu Wang, Lei Wei, Lei Wei, Jing Ma, John Easton, William R. Sellers, Nicholas Keen, Jun Liu, Jun Liu, Charles Mullighan, Steven Carr, James Downing, Levi Garraway, Frank Stegmeier. Global chromatin profiling identifies NSD2 mutations in pediatric acute lymphoblastic leukemia. [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 PR01.
Abstract A18: Time-resolved luminescence detection of spleen tyrosine kinase activity through terbium sensitization
Authors: Lipchik Andrew M. , Parker Laurie L. 
Published: August 2014

Abstract
Spleen tyrosine kinase (Syk) plays an important role in multiple B-cell signaling pathways. Deregulation of Syk activity has been shown to contribute to various malignant B-cell disorders including non-Hodgkin's lymphomas and chronic lymphocytic leukemia making Syk a potential drug target. However, monitoring the therapeutic response of Syk can be convoluted by the phosphorylation state of Syk or its downstream targets not always correlating with its enzymatic activity. Currently, there are few methods available for monitoring Syk activity directly. Peptide-based approaches allow for direct detection of kinase activity circumventing the need to assess phosphorylation status of the kinase. Peptides have been applied to the detection of Syk activity in the past using fluorescent amino acids, but these approaches have not yet reached an optimized degree of specificity or signal to noise.
Chelation with terbium has been used to achieve phosphorylation-dependent luminescence with substrate peptides. Terbium is a hard acid giving it preferred coordination with negatively charged species such as phosphate, carboxylate and carbonyl groups. Terbium as a luminescent probe for detection of phosphorylation offers several advantages over organic fluorophores. Terbium has unique optical properties including large stokes shifts, long luminescent lifetimes, and narrow emission bands. Recently, we have developed a Syk specific artificial substrate peptide (SAStide) consisting of an acidic motif with a central tyrosine capable of detecting intracellular Syk activity. We have characterized SAStide's ability to chelate terbium and sensitize terbium luminescence in a phosphorylation-dependent manner. Here we present the use of time-resolved luminescence through terbium sensitization for detection of Syk activity and inhibition using SAStide in vitro.
Citation Format: Andrew M. Lipchik, Laurie L. Parker. Time-resolved luminescence detection of spleen tyrosine kinase activity through terbium sensitization [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr A18.
Abstract A34: Novel chemical systems biology approach with the Berg Interrogative Biology® platform provides a window into hallmark shift in cancer metabolism
Authors: Narain Niven R. , Vishnudas Vivek K. , Akmaev Viatscheslav R. , Sarangarajan Rangaprasad 
Published: August 2014

Abstract
Cancer is comprised of a subset of diseases that serve to dysregulate the molecular mechanisms that maintain cellular homeostasis. Otto Warburg described his seminal observation that cancer cells negotiated a switch towards anaerobic respiration from oxidative phosphorylation in return for sustained growth and evasion of normal cellular processes such as cell cycle control and apoptosis. The underlying mechanism that governs this phenomenon has yet to be firmly established. We employed a chemical systems biology approach to create a mechanistic window into this phenomenon. Cancer models that encompass in vitro cancer and normal cell models, perturbants, and conditions including hypoxia, hyperglycemia, and redox environments that parallel cancer pathophysiology were overlayed and interrogated with an ubidecarenone-based epimetabolic shifter. Total cellular proteome including response to perturbants and chemical interrogation were assessed using LC MS based methods. Cell-based assays utilizing a Seahorse XF24 analyzer were employed to understand glycolytic fluxes and oxidative metabolism. High-throughput protein and metabolite data were subjected to an artificial intelligence-based informatics analysis that generated data driven inference of cause and effect maps of proteins interactome including inference of molecular networks driving metabolic endpoints. Follow-up network biology analysis revealed molecular interactions of differential response to epimetabolic shifts induced by ubidecarenone in normal and tumor cell models. Novel causal pathways that recapitulate the Warburg phenomenon by an amalgamation of nuclear, mitochondrial, and extracellular matrix components were derived and further validated by wet lab experiments. Finally we took a pan-disease approach that spanned cancer, diabetes, and neurodegenerative disease models and generated insights into overarching molecular entities that drive aberrant metabolism in various disease pathologies.
Citation Format: Niven R. Narain, Vivek K. Vishnudas, Viatscheslav R. Akmaev, Rangaprasad Sarangarajan. Novel chemical systems biology approach with the Berg Interrogative Biology® platform provides a window into hallmark shift in cancer metabolism [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr A34.