bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB-150: Genetic depletion of DNMT1 reveals a DNMT1 threshold controlling DNA methylation in human cells
Authors: Cai Yi , Tsai Hsing-chen , Yen Ray-whay , Xia Limin , Zhang Yang , Baylin Stephen 
Published: August 2015

Abstract
Altered DNA methylation patterns are a central feature of most types of human cancer cells. However, the exact roles of DNA methyltransferases (DNMTs) in human DNA methylation maintenance are not well characterized. The long-established model that DNA methyltransferase DNMT1 maintains most DNA methylation in human cells has been challenged by multiple DNMT1 knockdown/knockout studies in the past decade. A potential role for de novo DNA methyltransferases DNMT3A and DNMT3B in maintaining DNA methylation in cancer cells has been suggested but is also not precisely known.
To investigate the above issues, we have utilized both genetic recombination and CRISPR technology to deplete DNMTs individually or in combination in human colorectal cancer cell line HCT116. Previously we created a strong HCT116 DNMT1 hypomorph (1KO) by genetic recombination. Although 1KO cells lost about 85% of DNMT1 protein, they still maintained the epigenetic silencing of tumor suppressor genes and showed only 20% decrease in overall DNA methylation. We now show that further depletion of DNMT1 in 1KO cells, to less than 1% of wild type HCT116 cells, resulted in elimination of most DNA methylation and reactivation of key tumor suppressor genes including p16. In addition, we found that DNA methylation in HCT116 cells is controlled by different DNMT1 thresholds. Surprisingly, when we disrupted DNMT3A or DNMT3B with CRISPR in HCT116 cells, we see altered DNA methylation patterns involving both gains and losses of DNA methylation. Since abnormal DNA hypermethylation in cancer often associates with epigenetic gene silencing, this observation is especially relevant for the function of DNMT3A mutations in acute myeloid leukemia. Finally, we demonstrated that depletion of DNMT1-targeting protein UHRF1 efficiently reduced DNA methylation in human colon cancer cells. Our results not only defined the distinct roles of individual DNMTs in human cancer cell DNA methylation maintenance but also suggested UHRF1 inhibition as an alternative approach to reverse abnormal DNA hypermethylation in human cancer cells.
Citation Format: Yi Cai, Hsing-chen Tsai, Ray-whay Yen, Limin Xia, Yang Zhang, Stephen Baylin. Genetic depletion of DNMT1 reveals a DNMT1 threshold controlling DNA methylation in human cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-150. doi:10.1158/1538-7445.AM2015-LB-150
Abstract LB-153: In vivo visualization of the targeted DNA methylation
Authors: Chen Yao-Li , Chen Shou-Tung , Chung Chun-Chun , Hsu Chia-Chen , Lin Ping-Yi , Chuang Wan-Ling , Chu Yi-Ju , Leu Yu-Wei , Hsiao Shu-Huei 
Published: August 2015

Abstract
DNA methylation is a dominant silencing epigenetic modification that is inheritable in somatic cells. The recruitment of DNA methylation was proven to be able to reshape the cell physiology and cause tumorigenesis. The reversible nature of the methylation modification also makes the DNA methylation a therapeutic target and the monitoring of the methylation/demethylation dynamics in vivo is thus important for the development of demethylation agents. A targeted DNA methylation method and a two-component reporter system were combined to monitor the increase and demolishment of DNA methylation in vivo. The two constructs of the reporter systems are: target gene promoter (like HIC1 and ENSA) linked with the Tet repressor gene; the other is the Tet operator linked with the reporter like EGFP (in cell), IFP and iRFP. Both constructs were co-transfected into cells like mesenchymal stem cells, MDA-MB-231 and HCT116, and stable clones with both constructs were isolated and validated. Targeted DNA methylation method was used to transfect the isolated cell and, as the increase of DNA methylation, the reporters expressed. The increased methylation was then quenched after the adding of demethylation agents. To test this system in vivo, cells with both constructs were injected into the immune-deficient mice and the tumors grew afterward. Targeted DNA methylation was performed in vivo and the increase of methylation/expression of reporter genes were observed by fluorescence-based tomography. This combined system is also effective to monitor the demethylation effects of the demethylation agents. (Supported by: NSC- 102-2320-B-194-003-MY3 and NSC-102-2314-B-371- 003-MY3, MOST Taiwan)
Citation Format: Yao-Li Chen, Shou-Tung Chen, Chun-Chun Chung, Chia-Chen Hsu, Ping-Yi Lin, Wan-Ling Chuang, Yi-Ju Chu, Yu-Wei Leu, Shu-Huei Hsiao. In vivo visualization of the targeted DNA methylation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-153. doi:10.1158/1538-7445.AM2015-LB-153
Abstract LB-156: Increased Notch1 expression suppressed the growth but promoted the stemness of gastric cancer cells
Authors: Chiu Chia-Chen , Lo Chien-Ju , Shen Chien-Heng , Lu Chung-Kuang , Chou Jian-Liang , Chu Pei-Yi , Hsiao Shu-Huei , Tseng Min-Jen , Leu Yu-Wei , Hsu Chia-Chen 
Published: August 2015

Abstract
To explore if the Notch pathway were abnormally regulated during gastric tumorigenesis, abnormal DLL1 promoter methylation and inversely correlated mRNA expression were detected in cultured cell lines and patient samples. Elevated DLL1 expression was observed in gastric lesion like gastritis or erosion, but decreased DLL1 expression was detected in all four stages of gastric cancers (n = 44). To identify the effector genes and construct the possible Notch signaling network in gastric cancer, Myc-tagged Notch1 was overexpressed in gastric cancer cell line followed by the chromatin-immuno-precipitation sequencing (ChIP-seq) analysis. In ChIP-seq analysis, antibodies against Notch1, Rbpjκ, and Myc were used to identify the Notch1 targets while antibodies against trimethylated histone 3 at lysine 4 (H3K4me3) or lysine 27 (H3K27me3) were used to detect the associated epigenetic states. We found that the Notch1-overexpression suppressed the gastric tumoral growth, and the target loci-associated H3K4me3 (active chromatin) were reduced while the association with H3K27me3 (suppressive chromatin) were increased. Overall, the H3K4me3 and H3K27me3 combined bivalent marks were increased after Notch1-overexpression, and this was correlated with promoted stemness as indicated by the increased Oct4 and CD44 (reported gastric cancer stem cell like marker) expression. EZH2, a Polycomb protein, was found to be associated with Rbpjκ which further links the Notch signaling together with the maintenance of cell stemness. Therefore, Notch signaling might be critical for tumor formation in gastric cancer. (Supported by: NSC-102-2320-B-194-003-MY3 and NSC-102-2314-B-371-003-MY3, MOST Taiwan)
Citation Format: Chia-Chen Chiu, Chien-Ju Lo, Chien-Heng Shen, Chung-Kuang Lu, Jian-Liang Chou, Pei-Yi Chu, Shu-Huei Hsiao, Min-Jen Tseng, Yu-Wei Leu, Chia-Chen Hsu. Increased Notch1 expression suppressed the growth but promoted the stemness of gastric cancer cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-156. doi:10.1158/1538-7445.AM2015-LB-156
Abstract LB-162: Oxidative damage disrupts telomere integrity and leads to cell senescence
Authors: Tan Rong , Sun Luxi , Gao Ying , Lan Li 
Published: August 2015

Abstract
Cellular DNA is organized into chromosomes and capped by a unique nucleoprotein structure, the telomere. Both oxidative stress and telomere shortening/dysfunction cause aging-related degenerative pathologies and increase cancer risk. However, a direct connection between oxidative damage to telomeric DNA, comprising less than one percent of the genome, and telomere dysfunction has not been established. By fusing the KillerRed chromophore with the telomere repeat binding factor 1, TRF1, we developed a novel approach to generate localized damage to telomere DNA and to monitor the real time damage response at the single telomere level. We found that DNA damage at long telomeres in U2OS cells is not repaired efficiently compared to DNA damage in non-telomeric regions of the same length in heterochromatin. Telomeric DNA damage shortens the average length of telomeres and leads to cell senescence and cell death in U2OS, HeLa, and IMR90 cells, when DNA damage at non-telomeric regions is undetectable. Telomere-specific damage induces chromosomal aberrations, including signal-free ends and sister-chromatid fusions, distinct from the damage induced by ionizing irradiation. Taken together, our results demonstrate that oxidative damage induces telomere dysfunction and underline the importance of maintaining telomere integrity upon oxidative damage.
Note: This abstract was not presented at the meeting.
Citation Format: Rong Tan, Luxi Sun, Ying Gao, Li Lan. Oxidative damage disrupts telomere integrity and leads to cell senescence. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-162. doi:10.1158/1538-7445.AM2015-LB-162
Abstract LB-186: Fiber intake modulates the effect of alcohol on breast cancer
Authors: Romieu Isabelle 
Published: August 2015

Abstract
Alcohol intake has been related to an increase risk of breast cancer while dietary fiber intake has been inversely correlated to breast cancer risk. A beneficial effect of fiber on ethanol carcinogenesis through their impact on estrogen levels is still controversial.
The purpose of this study is to investigate the role of dietary fiber as potential modifying factors of the association of alcohol to breast cancer using data from the European Prospective Investigation into Cancer and Nutrition (EPIC) study.
A prospective observational study of 334,850 women aged 35-70 years at baseline enrolled in the ten countries of the EPIC study and followed up for 11.0 years on average was conducted. Information on fiber and alcohol intake at baseline and average lifetime alcohol intake were calculated from country-specific dietary and lifestyle questionnaires. Hazard ratios (HR) and 95% confidence intervals (CI) of developing invasive breast cancer according to different levels of alcohol and fiber intake were calculated.
During 3,670,439 person-years, 11,576 incident breast cancer cases were diagnosed. Among women with low intake of fiber (&lt;18.5 g/day), the risk of breast cancer per 10g/day of alcohol intake was 1.057 (1.032;1.082) while among women with high intake of fiber (&gt;24.2 g/day) the risk of breast cancer was 1.012 (0.983;0.1.04) (Test for interaction p = 0.01). This modulating effect was stronger for fiber from vegetables and for estrogen positive tumors.
Our results suggest that fiber intake may modulate the positive association of alcohol intake to breast cancer risk. Women should be advised to control their alcohol intake, and increase their intake of fiber.
Citation Format: Isabelle Romieu. Fiber intake modulates the effect of alcohol on breast cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-186. doi:10.1158/1538-7445.AM2015-LB-186
Abstract LB-201: Functional role for tumor heterogeneity: Paracrine signaling between tumor subclones of mouse SCLC promotes metastasis
Authors: Kwon Min Chul , Proost Natalie , Sutherland Kate , Zevenhoven John , Berns Anton 
Published: August 2015

Abstract
Tumor heterogeneity might not only lead to pools of cells with a different resistance profile to therapy, the heterogeneity can also create a unique tumor-microenvironment. Earlier we have shown that clonal evolution in mouse SCLC can result in subclones with either neuro-endocrine (NE) and non-NE features. Co-grafting of such subclones endow the NE tumor cells with metastatic potential. To address the underlying mechanism we conducted a series of in vivo graft experiments and found that non-cell autonomous paracrine signaling is required in the subcutaneously grafted tumor to permit dissemination. The expression of transcription factor Pea3 in NE cells was identified as a functional downstream target of this paracrine interaction between the tumor subclones. Fgf2 secreted by non-NE subclones causes the expression of Pea3 in the NE cells through activation of Mapk pathway thereby temporarily potentiating its invasive capacity and facilitating intravasation into the circulation. These findings reveal a cooperating role of tumor cell subclones in mouse SCLC. Our data indicate that inhibition of the Fgf2/Mapk/Pea3 axis might be exploited to impair growth and metastatic spread of SCLC. Given the similarity in phenotypic tumor cell heterogenenity and signaling aberrations between mouse and human SCLC, inhibition of this signaling axis is therefore worth exploring in human SCLC.
Citation Format: Min Chul Kwon, Natalie Proost, Kate Sutherland, John Zevenhoven, Anton Berns. Functional role for tumor heterogeneity: Paracrine signaling between tumor subclones of mouse SCLC promotes metastasis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-201. doi:10.1158/1538-7445.AM2015-LB-201
Abstract LB-229: Agonistic antibodies to costimulatory molecules, OX40 and GITR, significantly enhance the antitumor efficacy of Listeria monocytogenes (Lm-LLO)-based immunotherapy
Authors: Mkrtichyan Mikayel , Shrimali Rajeev , Ahmad Shamim , Abu Eid Rasha , Berrong Zuzana , Wallecha Anu , Petit Robert , Khleif Samir N. 
Published: August 2015

Abstract
Combinational anti-cancer immune therapies that target multiple tumor-mediated suppressive mechanisms or enhance effector immunity are emerging as promising strategies for cancer treatment. Recently, we demonstrated that the combination of Listeria monocytogenes (Lm-LLO)-based immunotherapy (ADXS11-001) and anti-PD-1 antibody results in improved anti-tumor therapeutic and immune efficacy. Interestingly, regardless of the presence of an antigen or treatment with anti-PD-1 antibody, treatment with the Lm-LLO alone significantly inhibited the suppressive arm of the immune system, including regulatory T cells and myeloid-derived suppressor cells. We therefore hypothesized that combination of ADXS11-001 with agonistic antibodies against co-stimulatory molecules will lead to further improvement of immune and therapeutic efficacy as a result of the combined down-regulation of the suppressive arm and the enhancement of the effector arm. Here we demonstrate that combining Lm-LLO-based immunotherapy with anti-OX40 or anti-GITR antibodies lead to significant inhibition of tumor growth and prolonged survival of animals. The complete regression of established TC-1 tumors occurs in 40% and 60% of animals treated with ADXS11-001 in combination with anti-OX40 and anti-GITR antibodies, respectively. We show that this therapeutic potency enhancement is due to a significant increase in antigen-specific immune responses along with ADXS11-001-mediated inhibition of suppressor cells. Thus, we believe that simultaneous stimulation of T cells while inhibiting the suppressor cells, specifically using Lm-LLO-based immunotherapy combination with agonistic anti-co-stimulatory molecule antibody is a feasible and translatable approach that can lead to overall enhancement of the efficacy of an anti-tumor immunotherapy.
Citation Format: Mikayel Mkrtichyan, Rajeev Shrimali, Shamim Ahmad, Rasha Abu Eid, Zuzana Berrong, Anu Wallecha, Robert Petit, Samir N. Khleif. Agonistic antibodies to costimulatory molecules, OX40 and GITR, significantly enhance the antitumor efficacy of Listeria monocytogenes (Lm-LLO)-based immunotherapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-229. doi:10.1158/1538-7445.AM2015-LB-229
Abstract LB-251: Histone deacetylase inhibition for the treatment of epithelioid sarcoma; novel cross talk between epigenetic components
Authors: Lopez Gonzalo , Song Yechun , Ruder Dennis , Creighton Chad Creighton , Bolshakov Svetlana , Zhang Xiaoli , Lev Dina , Pollock Raphael 
Published: August 2015

Abstract
Objective
Enhanced knowledge of epithelioid sarcoma (ES) molecular determinants will hopefully aid the development of urgently needed targeted therapies. The hallmark loss of INI1 causes a disruption in epigenetics, potentially contributing to the development of the disease. Recently, we have demonstrated that HDAC inhibitors (HDACi) to have efficacious value for the treatment various genetically complex sarcomas. Here, we aim to evaluate the potential therapeutic efficacy of HDACi in ES.
Methods
Three ES cell lines were used for this study: Epi-544, HS-ES, VAESBJ. MTS and clonogenic assays were utilized to evaluate the effect of HDACi on cell line growth. Cell cycle FACS and annexin V PI/FACS analysis with WB for cleaved caspase 3 were used to determine the effects of HDACi on cell cycle and apoptosis, respectively. In vivo growth effects of HDACi were evaluated using SCID mouse ES xenograft models. An Illumina gene array was used to evaluate HDACi-induced gene change.
Results
HDACi inhibited ES cell growth and colony formation. HDACi induced G2 cell cycle arrest and enhanced apoptosis in all ES cell lines tested. Similarly, HDACi abrogated ES xenograft growth and increased apoptosis in vivo. Due to the HDACi mechanisms of function, one of the major
consequences of this therapy is gene expression modulation. Using an Illumina gene array, we sought to identify genes responsible for the in vitro and in vivo anti-ES effects observed. Array analysis showed Survivin be significantly down-regulated in response to HDACi treatment. HDACi-induced decrease of Survivin was confirmed via WB. For enrichment analysis of our genes set with published annotated gene signatures, the Molecular Signatures Database (MSigDB) was used. MSigDB analysis identified a curated gene set of regulated genes after EZH2 knockdown (KD) with significant commonality of our gene array. We demonstrated HDACi-induced decrease of EZH2. EZH2 KD resulted in reduced cell growth and increased apoptosis in VAESBJ cells.
Conclusion
HDACs play a role in the progression of ES, where HDACi abrogate ES cell growth and enhance apoptosis in vitro and in vivo. Gene array analysis revealed various genes modulated by HDACi that may contribute to the progression of the disease. Anti-ES effects may be in part through the HDACi-induced repression of EZH2.
Citation Format: Gonzalo Lopez, Yechun Song, Dennis Ruder, Chad Creighton Creighton, Svetlana Bolshakov, Xiaoli Zhang, Dina Lev, Raphael Pollock. Histone deacetylase inhibition for the treatment of epithelioid sarcoma; novel cross talk between epigenetic components. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-251. doi:10.1158/1538-7445.AM2015-LB-251
Abstract LB-257: Discovery and characterization of novel, highly potent and selective USP7 inhibitors
Authors: Gavory Gerald , O'dowd Colin , McClelland Keeva , Odrzywol Ewa , Brown Alan , Burton Stephanie , Barker Oliver , Burkamp Frank , Helm Matt , James Iain , Flasz Jakub , Arkoudis Elias , Harrison Tim 
Published: August 2015

Abstract
Over the past decade, protein ubiquitination has emerged as an important post-translational modification with roles in a plethora of cellular processes, and dysregulation in the ubiquitin proteasome system pathway (UPS) has been implicated in multiple human disorders including cancer.
Ubiquitin specific proteases (USPs) are cysteine proteases that catalyse the de-ubiquitination of numerous protein substrates including tumor suppressors and oncogenes, hence regulating their levels and/or functions. USPs therefore represent a fast growing and attractive target class for pharmacological intervention. USP7 in particular has attracted considerable attention for its implications in multiple key oncogenic pathways including most notably MDM2/p53, PTEN and DNA damage.
As part of a focussed effort towards targeting USPs, fragment screening was performed against a panel of family members, including USP7. Hits were identified by surface plasmon resonance and validated using orthogonal biophysical techniques (NMR, thermophoresis). Subsequent hit expansion identified molecules for which high-resolution co-crystal structures have been solved providing unique opportunities for structure-based design.
Medicinal chemistry optimisation has yielded a series of novel, reversible and potent USP7 inhibitors (e.g. IC50 &lt; 10 nM) with excellent selectivity profiles against deubiquitinating (DUBs) and other non-related enzymes. These inhibitors are cell-permeable and also exhibit potent target engagement in cells (e.g. EC50 &lt; 30 nM). In line with the mechanism of action, further cellular profiling has demonstrated effects on p53, p21 and MDM2 levels in a concentration-dependant manner. From a translational viewpoint, initial studies aimed at identifying cell lines sensitive to these inhibitors will also be discussed.
In summary, we report the discovery and detailed biochemical and cellular profiling of novel, potent and selective inhibitors of USP7. These molecules have drug-like properties and may provide opportunities for the development of new anticancer therapeutics.
Citation Format: Gerald Gavory, Colin O'dowd, Keeva McClelland, Ewa Odrzywol, Alan Brown, Stephanie Burton, Oliver Barker, Frank Burkamp, Matt Helm, Iain James, Jakub Flasz, Elias Arkoudis, Tim Harrison. Discovery and characterization of novel, highly potent and selective USP7 inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-257. doi:10.1158/1538-7445.AM2015-LB-257