bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 486: BET protein inhibition by JQ1 blocks EWS-FLI1 activity in Ewing sarcoma
Authors: Bledsoe Krista L. , Stonestrom Aaron , Kadauke Stephan , Quick Laura , Young Robert , Blobel Gerd A. , Chou Margaret M. 
Published: August 2015

Abstract
Ewing sarcoma is the second most common bone cancer in children, with an estimated 5-year survival rate of 20% for metastatic cases. These tumors harbor the characteristic chromosomal translocation t(11;22)(q24;q12), which leads to expression of the oncogenic chimeric transcription factor, EWS-FLI1. EWS-FLI1 drives Ewing sarcoma tumorigenesis, and is an attractive therapeutic target because it is expressed exclusively in tumor cells. However, directly targeting EWS-FLI1 has proved difficult. Thus, despite advances in our understanding of EWS-FLI1 function, treatment options remain limited, and to date, no targeted therapeutics have been developed.
In this study, we investigated the effects of the epigenetic modifier drug, JQ1, on Ewing sarcoma pathogenesis. JQ1 is a small molecule inhibitor of the BET family of bromodomain proteins, which bind to acetylated histones and transcription factors to regulate gene expression. JQ1 selectively inhibits these acetylation-dependent BET protein interactions. Recent studies reveal that JQ1 has potent anti-neoplastic activity against multiple cancers, with c-MYC downregulation being a key mechanism by which it induces cell death in several tumor types. Because Ewing sarcoma cells express high levels of c-MYC, we predicted that they would be sensitive to the cytotoxic effects of JQ1.
Our results demonstrate that JQ1 indeed inhibits growth of Ewing sarcoma cells, but unexpectedly, it does not function through inhibition of c-MYC. Using multiple patient-derived Ewing sarcoma cell lines, we find that JQ1 induces apoptosis as measured by PARP cleavage. Preliminary data further indicate that JQ1 suppresses growth of Ewing sarcoma xenografts in vivo. Mechanistic studies and microarray analysis reveal that JQ1 inhibits EWS-FLI1 activity, with multiple targets of the oncogene being rapidly downregulated upon JQ1 treatment. Studies are currently underway to identify the specific BET family members required for EWS-FLI1 function, and to determine the mechanism by which they regulate EWS-FLI1 activity. Given the emergence of numerous JQ1-derivative compounds targeting specific BET proteins, it is hopeful that this class of compounds may ultimately be used as targeted therapies for the treatment of Ewing sarcoma.
Citation Format: Krista L. Bledsoe, Aaron Stonestrom, Stephan Kadauke, Laura Quick, Robert Young, Gerd A. Blobel, Margaret M. Chou. BET protein inhibition by JQ1 blocks EWS-FLI1 activity 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 486. doi:10.1158/1538-7445.AM2015-486
Abstract 488: High DKC1 expression supports neuroblastoma tumor cell proliferation and is strongly associated with poor patient outcomes
Authors: O'Brien Rosemary , Maritz Michelle F. , Kong Cheng Fei , Purgato Stefania , Liu Bing , Yang Chen , Russell Amanda , Murray Jayne , Flemming Claudia , Haber Michelle , Perini Giovanni , Norris Murray D. , Fletcher Jamie I. , Mackenzie Karen L. 
Published: August 2015

Abstract
Dyskerin is a nucleolar RNA-binding protein that functions as a core component of the telomerase holoenzyme, as well as in ribonuclear protein complexes involved in ribosome biogenesis and RNA processing. This study investigates the clinical and functional relevance of dyskerin expression in the paediatric cancer neuroblastoma. Here it is shown, in two independent neuroblastoma patient cohorts, that high expression of the gene encoding dyskerin (DKC1) very strongly correlates with poor event-free and overall survival. The prognostic power of DKC1 expression was independent of the established indicators used in the management of this disease, namely diagnosis age &gt; 1.5 yr, stage of disease and amplification of the MYCN oncogene (P&lt;0.0001). Dyskerin mRNA and protein expression were also found to be elevated, relative to normal cells, across a panel of neuroblastoma cell lines. Chromatin immunoprecipitation showed that the DKC1 promoter region was directly targeted by both MycN and c-Myc in neuroblastoma cells. Depletion of dyskerin using RNAi severely impaired proliferation, inhibited anchorage independent growth and dramatically slowed tumour growth in a mouse model of neuroblastoma (P&lt;0.01, Two-way Anova). In p53 competent cells, the proliferative arrest induced by dyskerin depletion was accompanied by an accumulation of p53 and p21cip1, accumulation in G1 phase of the cell cycle and cell death. However in the absence of p53 function, an alternate mechanism operated to impair proliferation when dyskerin was downregulated. The mechanism responsible for the proliferative arrest also appeared to be telomerase-independent, as it was not rescued by ectopic overexpression of telomerase. Taken together, these data identify DKC1 is a crucial MYC target gene in neuroblastoma, and show that neuroblastoma cells become addicted to high DKC1 expression. The results support further investigation of DKC1 as a therapeutic target in the treatment of refractory neuroblastoma.
Citation Format: Rosemary O'Brien, Michelle F. Maritz, Cheng Fei Kong, Stefania Purgato, Bing Liu, Chen Yang, Amanda Russell, Jayne Murray, Claudia Flemming, Michelle Haber, Giovanni Perini, Murray D. Norris, Jamie I. Fletcher, Karen L. Mackenzie. High DKC1 expression supports neuroblastoma tumor cell proliferation and is strongly associated with poor patient outcomes. [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 488. doi:10.1158/1538-7445.AM2015-488
Abstract 4904: Developing a universal target retrieval solution and protocol for RNA in situ hybridization based on RNAscope technology
Authors: Wang Li-chong , Pan Liuliu , Chang Kuang-Jung , Kim Daniel , Wu Xingyong , Wang Hongwei , Kernag Casey , Zhang Bingqing , He Mingxiao , Su Nan , Ma Xiao-Jun , Luo Yuling 
Published: August 2015

Abstract
Heat induced target retrieval (HITR) is a widely adopted approach for Immunohistochemistry (IHC) and in situ hybridization (ISH) applications on formalin fixed and paraffin embedded (FFPE) tissues to facilitate target access and increase detection sensitivity. A variety of factors, such as fixative type, fixation time, tissue type, epitope abundance, antibody affinity, and probe length greatly affect the efficiency of HITR. Given such variability, over the decades, multiple HITR buffer formulations and protocols were invented to fit the needs in different experimental scenarios.
We have developed a novel HITR solution that allows highly efficient target retrieval for RNA ISH application based on the RNAscope technology. When tested on 15 different tumor types, the new HITR solution resulted in significantly better sensitivity and/or tissue morphology comparing to using traditional HITR buffers, including Citrate, EDTA, and Tris based buffers with various pH. Furthermore, this new HITR solution is highly tolerant to sample variability. When used on multiple human tumor tissue microarrays (TMAs), including breast, colon, lung, and gastric cancers, the new HITR solution improved overall signal-to-noise ratio and reduced core disqualification rate, compared to traditional citrate based HITR buffer for ISH. Moreover, when tested on multiple mouse tissues fixed with different types of fixatives for varying periods of time (6 - 72 hours), a single experimental condition with the new HITR solution showed comparable results in both detection sensitivity and morphological integrity in all the samples. It also allowed detection of a target (Tbp) with extremely low abundance (&lt;5 copies/cell).
Given that all the RNAscope probes are synthetic oligonucleotide probes with length shorter than 60 bases, the new HITR solution, in combination with the RNAscope technology, will allow universal detection of any RNA targets with single molecule detection sensitivity in FFPE tissues with minimal requirement for analytical condition optimization.
Citation Format: Li-chong Wang, Liuliu Pan, Kuang-Jung Chang, Daniel Kim, Xingyong Wu, Hongwei Wang, Casey Kernag, Bingqing Zhang, Mingxiao He, Nan Su, Xiao-Jun Ma, Yuling Luo. Developing a universal target retrieval solution and protocol for RNA in situ hybridization based on RNAscope technology. [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 4904. doi:10.1158/1538-7445.AM2015-4904
Abstract 4915: Tracking genomic alterations in young patients with head and neck carcinomas using whole-exome sequencing
Authors: Miranda Priscila Mayrink , Marchi Fabio A. , Pinheiro Maísa , Kowalski Luiz Paulo , Rogatto Silvia Regina 
Published: August 2015

Abstract
Head and neck squamous cell carcinomas (HNSCC) often affect patients over 60 years, although epidemiological studies have shown an increased incidence in young adults (18-45 years), especially those having oropharynx and oral cavity tumors. There is no consensus regarding the etiology, clinical course and prognosis of HNSCC in young patients that often do not have the risk factors frequently described as associated with the disease (alcohol consumption, smoking and HPV infection). Despite its importance, studies with this group of patients are scarce, mainly focusing on the molecular aspects involved in the development and progression of the disease. In this study, we evaluated 36-paired samples (6 oral cavity, 12 oropharyngeal carcinomas and 18 matched blood samples) by whole exome sequencing (WES) aiming to identify molecular markers useful to clinical practice. Libraries were prepared (Illumina Nextera exome Enrichment kit) for WES using the high quality DNA from tumor tissue and peripheral blood of each patient (HiSeq2500, Illumina). The coverage reached an average of 55x per sample. We used an in-house pipeline for cleaning, mapping and SNP calling revealing an average of 36,494 SNPs per sample. A paired comparison of normal and tumor samples was performed considering only the exclusive variants in tumors, after exclusion of the common variants, based on 1000 Genomes (http://www.1000genomes.org/), project and 6500 exomes (evs.gs.washington.edu/). It was identified 248 variants distributed in 169 genes, with 184 (74%) classified as new (variant not described) and 64 (26%) as rare (population frequency ≤0.1%). Three genes, ZNF717, HYDIN and KCNJ12, presented higher frequency of SNPs and were enriched to head and neck carcinoma (p = 1,9×10-9) and calcium (p = 1.82×10-3) pathways. Considering only tongue samples (4 cases) from non-smokers and HPV negative patients, the ZNF717 and HYDIN genes remained among those with the highest frequency of SNPs [non-smokers: HYDIN (23 SNPs) and ZNF77 (24 SNPs); HPV-negative: HYDIN (6 SNPs) and ZNF77 (5 SNPs)]. These genes are putative drivers in young patients with HNSCC.
Financial Support: FAPESP (2013/06897-2) and INCiTO (FAPESP: 2008/57887-9 and CNPq 573589/08-9)
Citation Format: Priscila Mayrink Miranda, Fabio A. Marchi, Maísa Pinheiro, Luiz Paulo Kowalski, Silvia Regina Rogatto. Tracking genomic alterations in young patients with head and neck carcinomas using whole-exome sequencing. [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 4915. doi:10.1158/1538-7445.AM2015-4915
Abstract 4933: Sanger sequencing of low amount of genomic DNA and FFPE DNA with PCR primers derived from the Ion AmpliSeq cancer hotspot panel
Authors: Schreiber Edgar H. , Broomer Adam , Andersen Mark , Varma Kamini 
Published: August 2015

Abstract
The introduction of defined Ion AmpliSeq™ panels for detection and characterization of actionable mutations occurring in tumor tissue has the potential to revolutionize translational oncology research.
The Ion Ampliseq™ cancer hotspot panel version 2 (CHP v2) by Ion Torrent includes 207 actionable mutation targets present in 50 genes and the more comprehensive Ion Oncomine™ cancer panel (OCP) contains over 2000 mutations. A hallmark of these Ion Torrent Ampliseq cancer panels is the low amount of input DNA needed which is critical when the clinical specimen material is limited such as with fine needle biopsy or FFPE samples. Typically, 10 ng of DNA obtained from these sources is sufficient to produce informative sequencing data. Often, cancer-causing or promoting mutations are detected at relatively low allele frequencies like 10-20% compared to the major normal allele. Many researchers wish to verify these findings of low frequency mutations by an orthologous method such as traditional dye-fluorescent Sanger sequencing on a capillary electrophoresis (CE) instrument such as the Applied Biosystems 3500 genetic analyzer. To that end, we have developed a workflow that enables the amplification and traditional Sanger sequencing of individual Ion AmpliSeq targets directly from the AmpliSeq library starting material.
The method requires a retainer of 1 μl (∼ 5%) of the original AmpliSeq preamplification material. A dilution of this aliquot is used as template source for individualized PCR/sequencing reactions. We show that a random selection of 48 targets from the CHPv2 panel could be successfully amplified and Sanger-sequenced from an Ion Torrent Ampliseq library originally prepared from 10 ng of FFPE DNA. Furthermore, we show the successful Sanger-re-sequencing of all individual 24 targets covering the TP53 exons from the same sample processed and pre-amplified with the OncoMine AmpliSeq panel.
Taken together, this method will enable researchers to reflex-test potential mutations of interest from very material-limited specimen using Sanger CE sequencing.
Citation Format: Edgar H. Schreiber, Adam Broomer, Mark Andersen, Kamini Varma. Sanger sequencing of low amount of genomic DNA and FFPE DNA with PCR primers derived from the Ion AmpliSeq cancer hotspot panel. [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 4933. doi:10.1158/1538-7445.AM2015-4933
Abstract 494: MYC, dominant negative p53 and AKT transform human neural stem cells into primitive neuro-ectodermal tumors sensitive to glutaminase inhibitors
Authors: Taylor Isabella , Ahsan Sama , Price Antoinette , Eberhart Charles , Raabe Eric H. 
Published: August 2015

Abstract
Primitive neuroectodermal tumors (PNET) are highly aggressive tumors that can arise in different regions of the brain. A subset of PNET have genomic amplification of MYC, and the MYC-regulator LIN28A is known to define a group of PNET. Both MYC and LIN28 regulate metabolism in normal and malignant cells. We hypothesized that a combination of dominant negative R248Wp53, MYC, AKT and hTERT would transform human neural stem cells into PNET-like tumors. We used lentiviral vectors to infect human neural stem cells derived from hindbrain and cortex with the same packages of oncogenic elements. Hindbrain neural stem cells transduced with MYC/R248Wp53/AKT/hTERT proliferated at an increased rate compared to control cells as measured by BrdU incorporation (Hindbrain pBABE vs. Hindbrain MYC/R248Wp53/AKT/hTERT: 4% vs. 50% BrdU positive, t-test p = 0.001). Similar results were observed in cortex derived human neural stem cells transduced with MYC/R248Wp53/AKT/hTERT (Cortex pBABE vs Cortex MYC/R248Wp53/AKT/hTERT: 5% vs. 24% BrdU positive, t-test p = 0.027). Both hindbrain and cortex derived human neural stem cells transformed with MYC /R248Wp53/hTERT, and MYC/R248Wp53/hTERT/AKT formed aggressive orthotopic xenograft tumors with histologic characteristics of PNET. The latency of tumor formation decreased with increasing addition of oncogenes. We detected increased glutaminase (GLS) in our MYC-driven human neural stem cell models compared to SV40 immortalized neural stem cells, and hypothesized that GLS inhibitors would inhibit the growth of MYC-driven and LIN28 driven brain tumors. The glutaminase inhibitors DON (6-Diazo-5-oxo-L-norleucine) and acivicin suppressed the growth of our MYC-driven neural stem cell models of PNET as well as the PNET cell line PFSK (p = 0.003) as measured by BrdU and MTT growth assay. Cell cycle analysis of MYC-transduced human neural stem cell models showed increased cell death as measured by sub G1 population after treatment with DON and acivicin. This data shows that glutaminase inhibition may be a useful therapeutic modality in PNET.
Citation Format: Isabella Taylor, Sama Ahsan, Antoinette Price, Charles Eberhart, Eric H. Raabe. MYC, dominant negative p53 and AKT transform human neural stem cells into primitive neuro-ectodermal tumors sensitive to glutaminase 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 494. doi:10.1158/1538-7445.AM2015-494
Abstract 4958: Melanoma transition is frequently accompanied by a loss of cytoglobin, a putative tumor suppressor, in melanocytes
Authors: Fujita Yoshihiko , Koinuma Satoshi , De Velasco Marco , Jan Bolz , Togashi Yosuke , Terashima Masato , Hayashi Hidetoshi , Matsuo Takuya , Nishio Kazuto 
Published: August 2015

Abstract
Cytoglobin (CYGB), a new member of the globin family, remains to be characterized. To assess its expression in human malignancies, we screened a number of cell lines originated from many tissues, and found that several, but not all, melanoma cell lines expressed CYGB mRNA and protein at much higher levels than cells of other origins. Melanocytes, the primary origin of melanoma, also expressed CYGB at a high level. Bisulfite-modified genomic sequencing revealed that several melanoma cell lines that abrogated CYGB expression were found to be epigenetically regulated by hypermethylation in the promoter region of CYGB gene. The RNAi-mediated knockdown of the CYGB transcript in CYGB expression-positive melanoma cell lines resulted in increased proliferation in vitro and in vivo. Flow cytometric analysis using an indicator of reactive oxygen species (ROS) revealed that the CYGB knockown enhanced the cellular ROS level, which may be involved in the antiproliferative effect of CYGB. Thus, CYGB appears to play a tumor suppressive role as a ROS regulator, and its epigenetic silencing, as observed in CYGB expression-negative melanoma cell lines, might function as an alternative pathway in the melanocyte-to-melanoma transition.
Citation Format: Yoshihiko Fujita, Satoshi Koinuma, Marco De Velasco, Bolz Jan, Yosuke Togashi, Masato Terashima, Hidetoshi Hayashi, Takuya Matsuo, Kazuto Nishio. Melanoma transition is frequently accompanied by a loss of cytoglobin, a putative tumor suppressor, in melanocytes. [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 4958. doi:10.1158/1538-7445.AM2015-4958
Abstract 4969: Metformin causes AR degradation via Skp2-mediated ubiquitination
Authors: Yang Joy C. , Gao Allen C. , Evans Christopher P. 
Published: August 2015

Abstract
One of the mechanisms for prostate cancer cells to escape the new androgen receptor (AR) signaling inhibitor Enzalutamide (Enza) is through autophagy. Combination of anti-diabetic drug metformin with Enza demonstrated improved tumor suppression in the LNCaP C4-2B orthotopic model. Through delineating the mechanism in the metformin benefit, we discovered degradation of AR in cells treated with metformin alone and more in the combination with Enza and Abiraterone (Abi). The mRNA for AR in metformin-treated cells did not change significantly by qPCR assays. This degradation was inhibited when proteasome inhibitor MG132 was added prior to the treatments. Use of the FDA approved proteasome inhibitor Bortezomib also protected AR from degradation in the presence of metformin. Immunoprecipitation of AR with its antibodies showed ubiquitination; the reverse immunoprecipitation with anti-ubiquitin followed by anti-AR probing also showed similar results; suggesting ubiqutination responsible for AR degradation. With a paper by Li et al. proposing Skp2 being a novel E3 ubiquitin ligase targeting AR for ubiquitination, we attempted to knock-down Skp2 with transient siRNA transfection. Degradation of AR was lessened with Skp2 knockdown. This study supports that use of metformin in combination with Enza or other ARSI drugs may not only block autophagy survival but also cause AR degradation that leads to PC cell death.
Citation Format: Joy C. Yang, Allen C. Gao, Christopher P. Evans. Metformin causes AR degradation via Skp2-mediated ubiquitination. [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 4969. doi:10.1158/1538-7445.AM2015-4969
Abstract 4988: A7 nicotinic acetylcholine receptor mediated the chemosensitivity of gastric cancer cells
Authors: Huang Chien-Yu , Chang Yu-Jia 
Published: August 2015

Abstract
Background: Gastric cancer is important healthy issue in the worldwide. A7-nAChR has become a potential therapeutic target for cancer. Highly expression of A7-nAChR caused the benefit of cell survival in gastric cancers. However, it is unclear for the role of A7-nAChR in chemotherapy therapy on gastric cancer. Methods: In this study, we generated A7-nAChR knockdown (A7-nAChR-KD) AGS cells by a short interfering RNA (siRNA) technique in gastric cancer cells. The anti-proliferation effects of chemotherapy drugs were determined by biosensor system, MTT assay, TUNEL assay, and cell cycle determination.
Results: We determined the IC50 of 5-FU, taxane, epirubicin, cisplastin, gemcitabine, labtinibine, sunitinib in both A7-nAChR-Kd cells and scrambled control cells by MTT assay. We found that there is no difference between A7-nAChR-KD cells and scrambled control cells for epirubicin, cisplastin, labtinibine, sunitinib treatments. Interestingly, A7-nAChR-KD cells were less resistant to taxane treatment compared with the scrambled control cells. The apoptosis cell population was increased less in scrambled control cells treated with taxane than A7-nAChR-KD cells in cell cycle distribution and TUNEL assays. Conclusions: We conclude that A7-nAChR may be a key biomarker in mediating the chemotherapy efficacy on gastric cells.
Citation Format: Chien-Yu Huang, Yu-Jia Chang. A7 nicotinic acetylcholine receptor mediated the chemosensitivity 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 4988. doi:10.1158/1538-7445.AM2015-4988