bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-82: Chromosome 1q gain as genetic marker for risk stratification of pediatric ependymoma patients - validation as an adverse prognostic marker in the German multicenter HIT2000 trial.
Authors: Pietsch Torsten , Doerner Evelyn , zur Muehlen Anja , Velez-Char Natalia , Warmuth-Metz Monika , Kortmann Rolf-Dieter , von Hoff Katja , Friedrich Carsten , Rutkowski Stefan , von Bueren Andre O.
Published: August 2014

In contrast to histopathological grading which varied in respect to its prognostic value between different clinical trials, extent of resection was found to be consistently associated to the clinical outcome. In retrospective series, gain of genetic material of chromosome arm 1q was identified to predict worse outcome. This marker was mainly assessed by FISH analysis which typically showed failure rates of 15-20 % in archival material.

To validate this marker in a homogenously treated patient cohort, we analysed chromosome 1qin 209 consecutive cases enrolled into the multicenter trial HIT2000 (postoperative chemotherapy and irradiation, in a sequence depending on age and extent of resection) in which formalin-fixed, paraffin embedded material was available for DNA extraction. By using multiplex ligation-dependent probe amplification (MLPA) for 5 markers located on chromosome 1q and control markers, we were able to analyse 206/209 samples (> 98 %) and found a gain of chromosome 1q in 35 cases (17 %). 135/206 ependymomas were located in the infratentorial region. 35 cases were diagnosed as WHO grade II ependymoma, 171 as anaplastic ependymoma (WHO grade III). Interestingly, only 2 of the 35 WHO grade II ependymomas had 1q gain (5.7%).

At a median follow-up of 3.9 years for survivors, patients with tumors showing 1q gain had a significantly lower 4-year overall survival (OS) (±SE) of 58% +/- 9% compared to patients lacking this marker (89% +/- 3%, p=0.002). The distribution of this marker was similar when comparing patients with supra- and infratentorial tumors. Multivariable analysis demonstrated that residual tumor and infratentorial localization were independent risk factors for event-free survival, and gain of chromosome 1q for OS, respectively.

In conclusion, we validated chromosomal 1q gain to be a useful independent genetic marker for risk stratification of pediatric ependymoma patients which can be evaluated by MLPA representing a robust, reliable and cost-efficient method.

Citation Format: Torsten Pietsch, Evelyn Doerner, Anja zur Muehlen, Natalia Velez-Char, Monika Warmuth-Metz, Rolf-Dieter Kortmann, Katja von Hoff, Carsten Friedrich, Stefan Rutkowski, Andre O. von Bueren. Chromosome 1q gain as genetic marker for risk stratification of pediatric ependymoma patients - validation as an adverse prognostic marker in the German multicenter HIT2000 trial. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-82. doi:10.1158/1538-7445.AM2013-LB-82
Abstract LB-9: Mountain ginseng extract exhibits anti-lung cancer activity by inhibiting the nuclear translocation of NF-κB.
Authors: Jang Ik Soon , Park Junsoo , Lee Seung Hoon , Choi JongSoon
Published: August 2014

Administration of mountain ginseng (MG) extract can restore advanced cancer to a normal state. To elucidate the mechanism by which MG extract prevents the progression of lung cancer, the processes of proliferation and death of lung cancer cells (A549) were examined after treatment with MG extract. Butanol-extracted MG (BX-MG) showed a high inhibitory effect (IC(50) = 2 mg/ml) by attenuating proliferation and inducing apoptosis in lung cancer cells. By HPLC-UV analysis of BX-MG, ginsenosides, Rb1 was identified as the most abundant ginsenoside, followed by Rg1, Re, Rc and Rb2. BX-MG induced caspase-3 dependent apoptosis by inhibiting NF-κB. In addition, BX-MG activated p53 and p21, resulting in the attenuated proliferation of A549 cells. Reduced activity of the NF-κB promoter and increased activity of the p53 promoter indicate that BX-MG regulates apoptosis at the level of transcription in lung cancer cells. Furthermore, BX-MG blocked the nuclear translocation of RelA and the associated reduction in surviving. These results suggest that BX-MG inhibits lung cancer cell growth by activating tumor suppressors and inhibiting nuclear translocation of NF-κB.

Citation Format: Ik Soon Jang, Junsoo Park, Seung Hoon Lee, JongSoon Choi. Mountain ginseng extract exhibits anti-lung cancer activity by inhibiting the nuclear translocation of NF-κB. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-9. doi:10.1158/1538-7445.AM2013-LB-9
Abstract SY15-01: Merkel cell polyomavirus: its role in pathogenesis and its potential as a molecular target.
Authors: Chang Yuan
Published: August 2014

Merkel cell carcinoma (MCC) was first described as a pathologic entity in 1972, and is an uncommon but aggressive skin cancer with a high propensity for metastasis and recurrence. In 2008, a new human polyomavirus, Merkel cell polyomavirus (MCV) was discovered by digital transcriptome subtraction in an MCC lesion and is now one of eight new human polyomaviruses described in the past five years. MCV is part of the normal, healthy skin flora but causes cancer after viral genome mutations eliminate its replication capacity. Further, MCV is clonally integrated in 70-80% of MCC tumors suggesting a primary role for its involvement in MCV infected MCCs.

The MCV genome is ~5400bp and has features including early, late, and non-coding regulatory regions conserved with other polyomaviruses. The MCV early region encodes for two potential viral oncoproteins: large T antigen (LT) and small T antigen (ST). Experiments show these proteins are expressed in MCC tumor cells from patient biopsies, and that MCV-positive MCC cell lines undergo growth arrest and/or cell death upon T antigen knockdown by short hairpin RNA (shRNA). These experiments provide direct experimental evidence that T antigen expression is necessary for the maintenance of MCV-positive MCC and that MCV is the infectious cause of MCV-positive MCC.

While similar to known polyomaviruses, MCV oncogenes act in new ways, such as activation of the survivin oncoprotein and PP2A-independent targeting of cap-dependent translation. In five years, the diagnosis and treatment potential for an intractable and enigmatic cancer has dramatically changed through the discovery of a viral cause of MCC.

Citation Format: Yuan Chang. Merkel cell polyomavirus: its role in pathogenesis and its potential as a molecular target. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY15-01. doi:10.1158/1538-7445.AM2013-SY15-01
Abstract SY16-02: Embracing complexity: A drosophila approach to cancer therapeutics.
Authors: Cagan Ross L.
Published: August 2014

Cancer's complexity is a key difficulty in identifying useful therapeutics. In place of simplifying the disease, I will describe our use of Drosophila to develop complex, multigenic cancer models that directly reflect current human tumor sequencing data. These include colorectal, pancreatic, and thyroid tumor models. Further, I will discuss our approach– in collaboration with Kevan Shokat's laboratory– that combines fly genetics with medicinal chemistry to develop novel drugs through "rational polypharmacology," emphasizing a balance of "targets" and "anti-targets" that are designed to optimize therapeutic index.

Citation Format: Ross L. Cagan. Embracing complexity: A drosophila approach to cancer therapeutics. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY16-02. doi:10.1158/1538-7445.AM2013-SY16-02
Abstract SY18-04: Next-generation screens for cancer genes.
Authors: Adams David J.
Published: August 2014

In humans diverse mutagenic processes contribute to tumor development and drive tumor evolution. We have been performing genetic screens in mouse models of cancer engineered to carry known driver mutations. Using exome sequencing, whole genome sequencing, and transposons in these models we have identified genes that can promote tumorigenesis and regulate response to therapy. I will talk about our latest progress with these screens and the genes we have discovered.

Citation Format: David J. Adams. Next-generation screens for cancer genes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY18-04. doi:10.1158/1538-7445.AM2013-SY18-04
Abstract SY30-03: Monitoring tumor evolution by clonal tracking in ctDNA.
Authors: Caldas Carlos
Published: August 2014

Clonal evolution and the resulting tumor heterogeneity presents challenges for molecular diagnostics, tumor burden monitoring and studying mechanisms of drug resistance. In breast cancer circulating mutant cell free DNA (ctDNA) can be used as a ‘liquid biopsy’ to tackle all of these challenges. I will present our data that provides proof of principle for the use of ctDNA to track clonal evolution/clonal selection in both metastatic breast cancer and localized breast cancer treated with neo-adjuvant therapy.

Citation Format: Carlos Caldas. Monitoring tumor evolution by clonal tracking in ctDNA. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr SY30-03. doi:10.1158/1538-7445.AM2013-SY30-03
Abstract A12: Alkylation of histones by 4-oxo-2-nonenal as a novel modification linked to oxidative stress
Authors: Galligan J J. , Rose K L. , Beavers W N. , Aluise C D. , Shuck S C. , Marnett L J.
Published: August 2014

Sustained oxidative stress leads to the generation of toxic concentrations of the lipid aldehydes 4-hydroxy-2-nonenal (4-HNE) and 4-oxononenal (4-ONE), which are capable of covalently modifying the side-chains of Cys, His, and Lys residues. These protein modifications have been identified as a contributing factor in numerous disease states, including cancer, cardiovascular disease, neurodegeneration and diabetes. Here, we describe a novel class of histone modifications resulting from lipid electrophile adduction of His and Lys residues. Utilizing click chemistry with ω-alkynyl-4-ONE (a4-ONE), we have identified all-four core histones as targets for modification in RKO cells treated with physiologically relevant concentrations of electrophile. Isolation of chromatin from these cells reveals H2B as a highly susceptible target to modification by 4-ONE, while H2A, H3 and H4 show minimal reactivity. Interestingly, similar experiments with a4-HNE failed to identify any of the core histones as targets for modification. 4-HNE reacts heavily with Cys residues, which histones lack, whereas 4-ONE reacts primarily with the ϵ-amine of Lys residues. A proteomic investigation of site-specific modifications in RKO cells treated with 4-ONE reveals H2B Lys117 as a major target for modification. The predominant stable species detected on H2BK117 results from a 1,2-addition and net acylation analogous to Lys acetylation. H2BK117 is a surface exposed Lys residing on the face of the nucleosome core particle. Treatment of RKO cells with physiologically relevant doses of 4-ONE results in the altered expression of 40 genes. Electrophile adduction of histones provides a previously unexplored link between oxidative stress and gene regulation.

Citation Format: J J. Galligan, K L. Rose, W N. Beavers, C D. Aluise, S C. Shuck, L J. Marnett. Alkylation of histones by 4-oxo-2-nonenal as a novel modification linked to oxidative 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 A12.
Abstract A14: Understanding the role of ATRX in the development and progression of glioma
Authors: Goldberg Hannah E. , Kernohan Kristin D. , Berube Nathalie G.
Published: August 2014

Gliomas are tumors that arise from glial cells within the brain and spinal cord and account for approximately 30% of all central nervous system neoplasms. Emerging evidence indicates that unique molecular and genetic footprints define glioma subtypes. The Atrx gene is commonly mutated in a subset of gliomas across all tumor grades and within both the pediatric and adult populations. ATRX is a chromatin remodeling protein that is necessary for proper neural development. Loss of ATRX conditionally in the forebrain of the mouse starting at embryonic day 8.5 leads to an increase in replication stress and p53-mediated cortical cell death. Microarray analysis of control and Atrx-null neonatal forebrains indicates a significant increase in the expression of many cancer-related genes. Many of these overexpressed genes are involved in cellular migration, invasion, and epithelial-mesenchymal transition — important cellular phenotypes known to contribute to glioma development. Our data highlight oncogenic signaling pathways that become activated in the absence of the ATRX protein in the brain that may promote tumorigenesis when combined with additional genetic mutations, such as p53 mutations.

Citation Format: Hannah E. Goldberg, Kristin D. Kernohan, Nathalie G. Berube. Understanding the role of ATRX in the development and progression of glioma. [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 A14.
Abstract A30: Inhibiting histone methylation as an epigenetic therapeutic approach for pancreatic cancer
Authors: Govindarajan Rajgopal
Published: August 2014

We evaluated the potential of an investigational histone methylation reversal agent, 3-deazaneplanocin A (DZNep), in improving the chemosensitivity of pancreatic cancer to nucleoside analogs (i.e., gemcitabine). DZNep brought delayed but selective cytotoxicity to pancreatic cancer cells without affecting normal human pancreatic ductal epithelial (HPDE) cells. Co-exposure of DZNep and gemcitabine induced cytotoxic additivity or synergism in both well- and poorly-differentiated pancreatic cell lines. In contrast, DZNep exerted antagonism with gemcitabine against HPDE cells with significant reduction in cytotoxicity compared with the gemcitabine-alone regimen. DZNep marginally depended on purine nucleoside transporters for its cytotoxicity, but the transport dependence was circumvented by acyl derivatization. Drug exposure studies revealed that a short priming with DZNep followed by gemcitabine treatment rather than co-treatment of both agents to produce a maximal chemosensitization response in both gemcitabine-sensitive and gemcitabine-resistant pancreatic cancer cells. DZNep rapidly and reversibly decreased trimethylation of histone H3 lysine 27 but increased trimethylation of lysine 9 in an EZH2- and JMJD1A/2C-dependent manner, respectively. However, DZNep potentiation of nucleoside analog chemosensitization was found to be temporally coupled to trimethylation changes in lysine 27 and not lysine 9. Polymeric nanoparticles engineered to chronologically release DZNep followed by gemcitabine produced pronounced chemosensitization and dose-lowering effects. Together, our results identify that an optimized DZNep exposure can presensitize pancreatic cancer cells to anticancer nucleoside analogs through the reversal of histone methylation, emphasizing the promising clinical utilities of epigenetic reversal agents in future pancreatic cancer combination therapies.

Citation Format: Rajgopal Govindarajan. Inhibiting histone methylation as an epigenetic therapeutic approach for pancreatic 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 A30.
Abstract A46: LSD1 globally mediates epigenetic modifications on androgen receptor-dependent enhancers
Authors: Cai Changmeng , He Housheng Hansen , Brown Myles , Balk Steven P.
Published: August 2014

Androgen receptor (AR) belongs to nuclear receptor superfamily and plays pivotal roles in development of prostate and prostate cancer. The lignded AR binds to AR responsive elements (ARE) on the enhancers and mediates the transcription activity. AR binding on chromatin appears to depend on the binding of pioneer factor FOXA1, which recognizes the active sites marked with high level of mono- or di-methylation of Histon 3 lysine 4 (H3K4me1-2) and then make the site accessible for AR binding. However, the in depth mechanism how FOXA1 opens the enhancer and whether this results in further chromatin modification remains unclear. Through ChIP-seq studies coupled with gene expression array, we have found LSD1 (lysine specific demethylase 1) together with its binding partner CoRest were recruited by FOXA1 to the AR-dependent enhancer and its histone demethylation functions were then activated by liganded AR. This results in the loss of methylation marks and activation of gene transcription but not affecting AR binding or AR-mediated nucleosome dynamics. In contrast to this activator function, LSD1 can also formed corepressor complex to suppress the transcription of a subset of genes. This comprehensive study clearly suggested distinct roles of LSD1 as a coactivator versus a corepressor in different protein complexes therefore to mediate different cell functions.

Citation Format: Changmeng Cai, Housheng Hansen He, Myles Brown, Steven P. Balk. LSD1 globally mediates epigenetic modifications on androgen receptor-dependent enhancers. [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 A46.
Abstract A55: Histone deacetylase inhibitors as differentiation agents in breast cancer cells
Authors: Ismail Houssam , Bail Martine , Laperrière David , Hilmi Khalid , Mader Sylvie
Published: August 2014

FOXA1 and GATA3 are two luminal lineage transcription factors that form a cross-regulatory transcriptional network that controls the morphogenesis of the mammary gland and regulates estrogen receptor (ER) signaling. Approximately two thirds of breast tumors overexpress ER at the time of diagnosis. Antiestrogen therapy has been effective in blocking the proliferative effects of ER, but unfortunately a significant proportion of patients will relapse due to resistance. Histone deacetylase inhibitors (HDACis) have been shown to suppress ER expression in ER+ breast cancer cells and are currently being tested in clinical trials in combination with antiestrogens for treatment of ER+ breast tumors. Here, we report that the HDACi Trichostatin A (TSA) abrogates the expression of FOXA1 and GATA3, as well as that of ER in MCF-7 breast cancer cells. Using gene expression microarrays, we observed that several markers of lactogenic differentiation including the cholesterol biosynthesis pathway were induced by TSA treatment. Moreover, expression of ER, FOXA1 and GATA3 is reduced during lactation in the mouse mammary gland. Finally, overexpression of GATA3 in MCF-7 cells reduced the TSA-mediated induction of lactogenic markers, suggesting that GATA3 may act as a repressor of lactogenic differentiation. Altogether, our studies suggest that HDACi treatment partially mimics differentiation events taking place in ER+ cells during lactogenesis. Future experiments will examine the mechanisms and clinical relevance of the differentiation properties of HDACis.

Citation Format: Houssam Ismail, Martine Bail, David Laperrière, Khalid Hilmi, Sylvie Mader. Histone deacetylase inhibitors as differentiation agents in breast cancer 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 A55.
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

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

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

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

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

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

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

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

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

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

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.
Abstract IA11: Functionalization the cancer genome
Authors: Mills Gordon B. , Lu Yiling , Cheung Wai Ting , Scott Kenneth , Liang Han
Published: August 2014

As we begin to implement next-generation sequencing into patient care, a central challenge will involve determining which aberrations in a given tumor represent “drivers” that determine tumor behavior versus “passengers” resultant from the inherent instability of cancer genomes. Critically even within cancer genes, many aberrations could still be passengers. Indeed, given the broad landscape of aberrations in human tumors, it is possible that genomic aberrations in a cancer gene could be hypomorphs (decreasing activity of a tumor suppressor gene), hypermorphs (increasing activity of an oncogene) or neomorphs (changing function of the protein). Neomorphs such as those engendered by mutations in IDH1 in glioma could be particularly challenging as their therapeutics liabilities are not likely to be predictable from known functions of the wild-type protein. Targeting driver aberrations should improve outcomes for patients, while targeting passenger aberrations would be without benefit and may instead result in unnecessary toxicity and delay implementation of effective therapies. It will also be critical to select the drug or drugs most likely to benefit each patient based on underlying aberrations in their own tumor. Unfortunately, there is a complete lack of practical high-throughput platforms able to identify and select optimal therapies targeting driver aberrations.

We have implemented a high-throughput pipeline that consists of generation of patient tumor mutations in open reading frames (ORF) and determining the effect of shRNA, wild-type ORFs and mutant ORFs in the BAF3 IL3 dependent sensor line. Aberrations that increase cell viability and proliferation are established as stable lines. Stable lines are then probed with a chemical genomic library of tool compounds targeting critical pathways as well as through a high-throughput reverse phase protein array (RPPA) functional proteomics platform. The intersection of functional effects in the platforms identifies potential drivers and elicits their mechanistic activity and potential therapeutic liabilities. This pipeline has the potential to elicit tumor drivers and identify individualized therapeutic approaches.

Citation Format: Gordon B. Mills, Yiling Lu, Wai Ting Cheung, Kenneth Scott, Han Liang. Functionalization the cancer genome [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 IA11.