bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4754: Development of fluorescent probes for detection of DNA base excision repair in human cancer cells
Authors: Condie Allison G. , Yan Yan , Gerson Stanton L. , Wang Yanming 
Published: August 2015

Abstract
Many cancer chemotherapeutics target DNA, which makes them vulnerable to repair by innate mechanisms the cell has evolved to ward off endogenous and exogenous DNA damage. In the course of chemotherapy, these repair pathways lead to drug resistance and reduced efficacy of cancer treatment. To address these issues, our goal was to develop imaging agents to visualize and quantify DNA repair in cancer. Thus, we have developed small molecule, fluorescent probes that bind to the abasic (or AP for apurinic/apyrimidinic) site in DNA, a key intermediate in the base excision repair (BER) pathway.
Taking advantage of the biochemistry of BER, we have developed an assay based on a fluorescently tagged DNA oligomer to evaluate the ability of these probes to bind to AP sites and stall further repair. This assay relies on blocking the DNA single strand breaking activity of the enzyme, AP endonuclease (APE), when its natural substrate, the AP site, is obstructed by probe binding. Using this assay, we have screened our novel probes for their AP site binding potential. Our cyanine-(Cy7) based probe outperformed other, commercially available AP site binding probes including methoxyamine (MX) and aldehyde reactive probe (ARP).
In addition, we have developed a method for analyzing a genomic DNA sample that demonstrates the potential to evaluate physiologically relevant quantities of AP sites. 5-Fluoro-2′-deoxyuridine (FUDR) is indicated for treatment of many types of cancer; however, uracil DNA glycosylase (UDG) can repair the lesions in DNA introduced by FUDR. Therefore, we prepared a UDG knockdown of the DLD1 colon cancer cell line and treated both wild type and knockdown cells with FUDR for 24, 48, and 72 h. Following extraction of the DNA and in vitro treatment with purified UDG, we observed a nearly 9-fold increase in fluorescence in treated versus untreated cells. This confirmed that our probe could report of AP site quantity in cancer cells in vitro.
Our cyanine-based probes have several benefits over existing probes including red and NIR fluorescence for application in animal imaging. Our studies indicate that these probes bind to AP sites more efficiently than existing probes. Further, these fluorescent AP site-binding agents could have application in drug development and discovery or be used in assays to monitor patient response to therapy.
Citation Format: Allison G. Condie, Yan Yan, Stanton L. Gerson, Yanming Wang. Development of fluorescent probes for detection of DNA base excision repair in human 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 4754. doi:10.1158/1538-7445.AM2015-4754
Abstract 4756: Genomic profile of AML-ETO rearranged acute myeloid leukemia
Authors: Koh Youngil , Kim Dae-Yoon , Kim Jong-Kwang , Chung Yeun-June , Yoon Sung-Soo , Kim Hyung-Lae 
Published: August 2015

Abstract
Introduction
Although it is well known that core-binding factor(CBF) acute myeloid leukemia(AML) harbors good prognosis, some patients with CBF-AML have dismal outcome. In this study, we tried to find out genomic alterations in CBF-AML so as to find genetic changes that determine prognosis of CBF-AML.
Materials and methods
We performed whole genome sequencing (WGS) of 9 AML-ETO rearranged AML patients. For whole genome sequencing, we used Hiseq 2000 (Illumina, SanDiego, CA, USA). Single nucleotide variant (SNV) calling was performed using 4 different callers. Structural variant calling was performed using three different callers.
Results
Among 9 patients, two patients had excellent prognosis, while 3 patients showed unfavorable outcome with conventional chemotherapy. 4 patients had undetermined prognosis. As for SNV, the most frequent common non-synonymous SNV was KIT mutation, while ADAMTS17 and CFAP46 mutation was found in 2/9 patients respectively. Noticeable non-synonymous SNV found only in patients with poor prognosis included NRAS, ADAM29, AGO1, and ALAS2 mutation. For structural variation, LOC44166 inversion, ANKRD26P1 deletion, EMBP1 translocation were noticeable structural variants other than AML-ETO rearrangement in these patients.
Conclusion
Not a single genetic factor was attributable to the prognosis in CBF-AML. Further validation of genetic alterations found study in this study is ongoing.
Citation Format: Youngil Koh, Dae-Yoon Kim, Jong-Kwang Kim, Yeun-June Chung, Sung-Soo Yoon, Hyung-Lae Kim. Genomic profile of AML-ETO rearranged acute myeloid leukemia. [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 4756. doi:10.1158/1538-7445.AM2015-4756
Abstract 4759: Whole genome sequencing of sequentially acquired lung and lymph node metastatic sites from a never smoker lung adenocarcinoma patient revealed extensive genomic heterogeneity
Authors: Gao Shaojian , Cultraro Constance , BIswas Romi , Carter Corey A. , Maity Tapan K. , Thomas Anish , Rajan Arun , Meltzer Paul , Schrump David , Giaccone Giuseppe , Khan Javed , Guha Udayan 
Published: August 2015

Abstract
Recent large-scale cancer genome sequencing studies have uncovered extensive diverse mutational landscapes in lung cancer patients. Furthermore, tumor heterogeneity has been widely recognized and it has significant clinical implications in selection of targeted treatment strategies as well as treatment response. Using whole genome sequencing, we demonstrate an unprecedented genomic heterogeneity between sequentially acquired lung and lymph node metastatic sites from an African American never-smoker lung adenocarcinoma patient who has survived with metastatic disease for over seven years while being treated with single or combination HER2-directed therapies. We determined that less than 1% of somatic variants were common between the two tumor sites. Copy number variations were more intense in the lung tumor than in the metastatic lymph node. We identified several novel somatic mutations in key cancer genes in both sites. Interestingly, one novel translocation, PLAG1-ACTA2 was highly expressed in both the lung and lymph node metastases resulting in overexpression of ACTA2, which has been suggested to increase the metastatic potential in lung adenocarcinoma. Using ultra deep targeted re-sequencing, we validated all non-synonymous variants, and approximately 80% of those identified in the metastatic lymph node were also present in a second lymph node biopsied two years after the first one. Although this degree of tumor heterogeneity was surprising, somatic variants affected key hallmarks of tumorigenesis in both sites. These findings suggest a model of early metastatic spread and parallel clonal evolution in disparate metastatic sites.
Citation Format: Shaojian Gao, Constance Cultraro, Romi BIswas, Corey A. Carter, Tapan K. Maity, Anish Thomas, Arun Rajan, Paul Meltzer, David Schrump, Giuseppe Giaccone, Javed Khan, Udayan Guha. Whole genome sequencing of sequentially acquired lung and lymph node metastatic sites from a never smoker lung adenocarcinoma patient revealed extensive genomic heterogeneity. [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 4759. doi:10.1158/1538-7445.AM2015-4759
Abstract 4764: The Bromodomain inhibitors regulate long noncoding RNAs controlling glioblastoma progression
Authors: Pastori Chiara , Kapranov Philip , Penas Clara , Laurent Georges St. , Ayad Nagi , Wahlestedt Claes 
Published: August 2015

Abstract
Bromodomain and extra-terminal domain (BET) proteins have emerged as promising therapeutic targets in glioblastoma and many other cancers. Small molecule mimics of acetylated histones inhibit BET protein function and reduce expression of several oncogenes required for glioblastoma (GBM) progression. However, the mechanism through which BET protein inhibition reduces GBM growth is not completely understood. Long noncoding RNAs (lncRNAs) are important epigenetic regulators with critical roles in cancer initiation and malignant progression but mechanistic insight into their expression and regulation by bromodomain inhibitors remains elusive. In this study we utilized single molecule sequencing (SMS) to comprehensively profile lncRNAs differentially expressed in GBM and we identified a subset of GBM-specific lncRNAs whose expression is regulated by BET proteins. Treatment of GBM cells with the BET protein inhibitor I-BET151 reduced levels of the tumor-promoting lncRNA HOTAIR and restored the expression of several other GBM-down-regulated lncRNAs. Conversely, overexpression of HOTAIR in conjunction with I-BET treatment rescues the antiproliferative activity of I-BET151. Moreover, chromatin immunoprecipitation analysis demonstrated binding of Brd4 to the HOTAIR promoter suggesting that BET proteins can directly regulate lncRNA expression. Our data unravel a previously unappreciated mechanism through which BET proteins control tumor growth of glioblastoma cells and suggest that lncRNA networks may, in part, mediate the anti-proliferative effects of many epigenetic inhibitors currently in clinical trials for cancer and other diseases.
Note: This abstract was not presented at the meeting.
Citation Format: Chiara Pastori, Philip Kapranov, Clara Penas, Georges St.Laurent,Nagi Ayad, Claes Wahlestedt. The Bromodomain inhibitors regulate long noncoding RNAs controlling glioblastoma progression. [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 4764. doi:10.1158/1538-7445.AM2015-4764
Abstract 4767: DNA sequences differentially associated with Sirt1 and Dnmt3b during melanoma progression
Authors: Marcelino Meliso Fabiana , da Silva Camila Tainah , Coetzee Simon , Sarraf Sabedot Thaís , Noushmehr Houtan , Schneider-Stock Regine , Galvonas Jasiulionis Miriam 
Published: August 2015

Abstract
Melanoma is one of the most worrying tumors due to its high capacity to cause metastasis. Sirt1, a class III histone deacetylase, was shown to be attracted to sites of double strand breaks in DNA, favoring, by recruiting components of the epigenetic machinery, aberrant epigenetic silencing in that region (O’HAGAN et al., 2008). Beyond that, subsequent studies have attributed important roles of Sirt1 and other components of the epigenetic machinery, such as DNA methyltransferases (such as Dnmt3b), in tumor initiation and progression. In this sense, using a murine model of malignant transformation of melanocytes, associated with sustained stress conditions, our goal was to identify genomic sequences differentially associated to Sirt1 and/or Dnmt3B before and after stress condition, represented in our model by anchorage blockade, and analyze if these sequences are targeted by aberrant methylation in cell lines obtained by this process that represent different steps in melanoma progression. We have showed increased DNA damage after 24 hours of anchorage impediment followed by increased Sirt1 expression. In addition, we have showed Sirt1/Dnmt3b association just after this stress condition that leads to malignant transformation. It was identified several DNA sequences differentially associated to Sirt1 and also to Dnmt3b after stress condition which are also associated to genes related to different metabolic processes. Some of these sequences remain associated to Sirt1 and Dnmt3b during melanoma progression, indicating that Dnmt3b remains associated to Sirt1 during malignant transformation. Among the sequences, Tiam1 and Mxd1 are potential targets of Sirt1 and Dnmt3b that have important roles in tumor progression. We have also identified motifs where Sirt1 and Dnmt3b are probably bound before and after stress condition. The main motif related to Sirt1 was coincident with Boris motif. Subsequent analysis are been developed to elucidate the importance of these interesting discoveries. Supported by FAPESP and DAAD.
Citation Format: Fabiana Marcelino Meliso, Camila Tainah da Silva, Simon Coetzee, Thaís Sarraf Sabedot, Houtan Noushmehr, Regine Schneider-Stock, Miriam Galvonas Jasiulionis. DNA sequences differentially associated with Sirt1 and Dnmt3b during melanoma progression. [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 4767. doi:10.1158/1538-7445.AM2015-4767
Abstract 4774: Histone H2AX is a novel regulator of epithelial to mesenchymal transition
Authors: WEYEMI SOSSOU U. , Redon Christophe E. , Choudhuri Rohini , Maeda Daisuke , Kasoji Manjula , Abrams Natalie , Bonner William M. 
Published: August 2015

Abstract
The vast majority of deaths from cancer are due to its progression from primary tumor to metastatic disease. Understanding how some cells can migrate from the primary tumor to seed new tumors throughout the body is a longstanding challenge in developing novel cancer treatments. Current models propose that these migratory cells acquire an invasive phenotype through a process known as the epithelial to mesenchymal transition (EMT), characterized by the loss of cell polarity and cell-to-cell adhesion, and the acquisition of migratory and invasive properties. Such changes allow the cells to invade the extracellular matrix and migrate throughout the body, aided by the formation of lamellipodia, filopodia and invadopodia. In a converse transition, the MET, mesenchymal cells may revert back to the epithelial phenotype and establish tumors at distant sites.We have preliminary observations showing that when one member of the H2A family of histones, H2AX, is silenced or inactivated in HCT116 cells, these cells exhibit mesenchymal-like characteristics including increased invasiveness. Furthermore, genome-wide expression analysis implicates the critical EMT transcription factors, SLUG and ZEB1, as mediators of H2AX loss-induced EMT. To make these studies more rigorous, we generated a novel HCT116 cell line with H2AX destroyed. Our findings show that ectopic expression of H2AX in H2AX-null cells reverses the invasiveness induced by H2AX inactivation. Moreover, in 233 human colon cancer samples, a strong correlation is found between the levels of H2AX and SLUG/ZEB1 expression. These observations lead us to hypothesize that H2AX is a key regulator of EMT and plays a critical role in the downstream events leading to increased metastasis.
Note: This abstract was not presented at the meeting.
Citation Format: SOSSOU U. WEYEMI, Christophe E. Redon, Rohini Choudhuri, Daisuke Maeda, Manjula Kasoji, Natalie Abrams, William M. Bonner. Histone H2AX is a novel regulator of epithelial to mesenchymal transition. [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 4774. doi:10.1158/1538-7445.AM2015-4774
Abstract 4777: Triptolide inhibits Wnt signaling due to DNA methylation alteration that is determined by dynamic histone 3 K79 lysine methylation in NSCLC
Authors: Li Youqiang , Shen Binghui , Kim Jae , Raz Dan 
Published: August 2015

Abstract
Epigenetic alterations including DNA methylation and histone modifications have been associated with virtually every step of tumor development and progression. This realization has triggered an impressive quest for the development of “epigenetic drugs” and epigenetic therapies. Here we present data demonstrating that triptolide, with a unique mechanism, has anticancer effect in lung cancer development and progression. With the use of our unique non-small cell lung cancer (NSCLC) mouse model (ED160, Fen1 mutation), data shows triptolide decreases lung cancer incidence from 70% to 10%. In addition, triptolide effectively inhibits lung cancer growth and metastasis in NSG mouse Xenograft. Triptolide inactivates Wnt signaling by restoring WIF1 expression which is due to WIF1 gene demethylation. Furthermore, we revealed histone 3 lysine methylation alteration determines DNA methylation status by the communication between DNMT1 and histone 3. Together, these evidences indicated that sequential histone and DNA methylation active Wnt signaling; further it contributes to NSCLC development and progression. This discovery potentially is yielding epigenetic therapeutic opportunities for NSCLC.
Note: This abstract was not presented at the meeting.
Citation Format: Youqiang Li, Binghui Shen, Jae Kim, Dan Raz. Triptolide inhibits Wnt signaling due to DNA methylation alteration that is determined by dynamic histone 3 K79 lysine methylation in NSCLC. [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 4777. doi:10.1158/1538-7445.AM2015-4777
Abstract 478: EWS/FLI1 transcription is modulated by the PI3K pathway via SP1 in Ewing sarcoma
Authors: Giorgi Chiara , Boro Alexander , Lopez-Garcia Laura A. , Schaefer Beat W. , Niggli Felix K. 
Published: August 2015

Abstract
Ewing sarcoma (ES) is the second most frequent bone cancer in childhood and it is characterized by the presence of the balanced t(11;22)(q24;q12) translocation in more than 85% of cases, generating a dysregulated transcription factor EWS/FLI1. ES belongs to small-round-blue-cell tumors and it is a very aggressive osteolytic cancer with early tendency for development of metastasis. Mostly it affects bones such as pelvis, femour and ribs but can also arise in soft tissues, mainly in adults. EWS/FLI1 is an essential oncogenic component of ES development which is necessary for tumor cell maintenance, through inappropriate regulation of target genes that are crucial for the fully malignant phenotype. Therefore, EWS/FLI1 represents an attractive therapeutic target. Screening of a small library of 153 targeted compounds has identified inhibitors of the PI3K pathway as main modulators of EWS/FLI1 activity and surprisingly this was due to an effect of the compound on EWS/FLI1 transcription. Indeed, treatment of four different ES cell lines with BEZ235 (PI3K-mTOR inhibitor) resulted in downregulation of EWS/FLI1 by 50% expression with subsequent modulation of target gene expression. Analysis of the EWS/FLI1 promoter region (-2239/+67) using various deletion constructs identified two 14bp minimal elements, named Del2 and Del23 region, as being important for EWS/FLI1 transcription. Based on in silico prediction and on in vivo data, we were able to predict 4 transcription factor candidates to bind this region and being responsive to PI3K regulation. Among these, SP1 was identified as modulator of EWS/FLI1 gene expression by siRNA. Various approches such as qRT-PCR, Western Blot and Immunofluorescence confirmed a reduction of EWS/FLI1 in Ewing cells when PI3Kαγδ and SP1 were depleted; Electrophoretic Mobility Shift Assay (EMSA) and Chromatine Immuno Precipitation (ChIP) both confirmed that the transcription factor SP1 is indeed binding to Del23 region of the EWS/FLI1 promoter. In summary, our results provide the very first insights on the transcriptional regulation of EWS/FLI1, an area that has not been investigated so far, and offer a molecular explanation for the known sensitivity of ES cell lines to PI3K inhibition.
Citation Format: Chiara Giorgi, Alexander Boro, Laura A. Lopez-Garcia, Beat W. Schaefer, Felix K. Niggli. EWS/FLI1 transcription is modulated by the PI3K pathway via SP1 in Ewing sarcoma. [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 478. doi:10.1158/1538-7445.AM2015-478
Abstract 4780: Nucleosome organization and accessibility of p53 response elements in the chromatin context
Authors: LoVerso Peter R. , Zhurkin Victor B. , Cui Feng 
Published: August 2015

Abstract
p53 is one of best known human proteins that induces or represses hundreds of genes and plays a pivotal role in preventing tumor development. Recent studies established unambiguously that p53 is a nucleosome-binding protein. The rotational positioning of a nucleosome is critical to determine the accessibility of a p53 site. In particular, the p53 site in a nucleosome is accessible if it is bent in the direction similar to that found in the p53-DNA co-crystals; the site becomes inaccessible if the orientation is changed by ∼180°. Importantly, we have shown that p53 response elements (REs) associated with cell cycle arrest are often exposed on the nucleosomal surface, suggesting a new role of nucleosomes in mediating the p53 binding and subsequent gene induction.
The present study aims to make a detailed analysis of nucleosome organization of all p53 functional REs in normal and cancer cells. Published genome-wide nucleosome maps from lymphoblastoid (normal) and K562 (cancer) cell lines are used. In general, the p53 REs are located in nucleosome-enriched regions, in accordance with previous findings that p53 can interact with nucleosomal DNA. At the level of individual sites, the p21 5′ RE resides in a genomic region with high nucleosome occupancy, consistent with earlier studies. The GADD45 RE that was believed to be in nucleosome-free region, is, however, characterized with medium-to-high nucleosome occupancy.
To evaluate the accessibility of p53 REs in different functional groups such as cell cycle arrest, apoptosis and DNA repair, we used a more rigorous set of nucleosomes, containing 134 million 147-bp fragments (about 7x genome coverage). The REs in the cell cycle arrest group (such as p21) and the DNA repair group (such as GADD45) are often accessible in the chromatin context, consistent with fast induction of these genes after p53 activation. Interestingly, apoptotic REs are divided - the REs associated with the mitochondrial pathway (BAX and p53AIP1) are accessible, while the REs associated with the death receptor pathway (FAS and KILLER) are inaccessible, suggesting different mechanisms for induction of apoptotic genes in vivo.
Finally, we observe a clear correlation between the nucleosome occupancy and accessibility of p53 REs. That is, the REs with the higher nucleosome occupancy tend to be accessible, while the REs with lower nucleosome occupancy are likely to be inaccessible to p53.
Citation Format: Peter R. LoVerso, Victor B. Zhurkin, Feng Cui. Nucleosome organization and accessibility of p53 response elements in the chromatin context. [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 4780. doi:10.1158/1538-7445.AM2015-4780