bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3575: Ferroptosis: A novel nonapoptotic cell death overcomes head and neck cancer resistance to cisplatin
Authors: Jang Hye Jin , Park Jin Young , Kim Eun Hye , Kim Ji Won , Kwon Minsu , Roh Jong-Lyel 
Published: July 2016

Abstract
Ferroptosis was recently identified as a novel form of iron-dependent cell death different from apoptosis or necrosis. Inhibition of key molecules related to ferroptosis, cystine-glutamate antiporter (xCT) and glutathione peroxidase (GPX4), may induce the eradication of cancer cells resistant to conventional chemotherapy or radiotherapy. The present study investigated whether ferroptosis overcome head and neck cancer (HNC) resistant to cisplatin treatment. Three cisplatin-resistant HNC cell lines (AMC-HN3R, -HN4R and -HN9R), their parental lines, and other human HNC lines were used. The effects of cysteine and glutamate alteration and pharmacological and genetic inhibition of xCT were assess by measuring viability, death, total and cytoplasmic lipid reactive oxygen species (ROS) production, mitochondrial membrane potential (ΔΨm), protein expression, and preclinical mouse tumor xenograft models. Conditioned media with no cysteine or high glutamate supplement induced ferroptosis of both cisplatin-sensitive and -resistant HNC cells without apparent change of necrosis and apoptosis markers, RIP1 and RIP3 and casplase-3 expression, and ΔΨm. This was blocked by antioxidants trolox or N-acetyl cysteine pretreatment. Sulfasalazine, artensunate, and erastin inhibited the growth of HNC cells and accumulated cytoplasmic lipid ROS via induction of ferroptosis and inhibition of xCT protein expression. Genetic silencing of xCT with siRNA or shRNA treatment also induced the effective cell death (ferroptosis) of resistant HNC cells. These effects were blocked with trolox or ferrostatin-1 pretreatment. Pharmacological and genetic inhibition of xCT significantly sensitized resistant HNC cells to cisplatin in vitro and in vivo. Cystine deficiency or glutamate excess induces ferroptosis in HNC cells. Further, pharmacological and genetic inhibition of xCT overcomes the cisplatin resistance of HNC cells by inducing ferroptosis.
Citation Format: Hye Jin Jang, Jin Young Park, Eun Hye Kim, Ji Won Kim, Minsu Kwon, Jong-Lyel Roh. Ferroptosis: A novel nonapoptotic cell death overcomes head and neck cancer resistance to cisplatin. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3575.
Abstract 3577: Pan-cancer analysis of mutagenesis by APOBEC cytidine deaminases
Authors: Gordenin Dmitry A. 
Published: July 2016

Abstract
The elucidation of mutagenic processes that shape cancer genomes is a fundamental problem whose solution promises insights into new treatment, diagnostic, and prevention strategies. We and others previously identified mutation clusters and genome-wide mutagenesis bearing the single-strand DNA (ssDNA)-specific APOBEC cytidine deaminase signature at 5′-tC-3′ motifs across many cancer types. Because of high abundance of APOBEC mutagenesis in several cancer types, we have developed a statistical approach capable of identifying cancer samples with APOBEC mutagenesis pattern based on WGS as well as on WES mutation data. This analysis, called Pattern of Mutagenesis by APOBEC Cytidine Deaminases (P-MACD), has been recently integrated into the Broad Institute GDAC Firehose and is currently available for Firehose standard and AWG-customized runs. The results of analysis using the P-MACD package will be discussed, including correlations with molecular and clinical features of TCGA cancer samples as well as relative roles of different APOBEC enzymes in cancer mutagenesis.
Citation Format: Dmitry A. Gordenin. Pan-cancer analysis of mutagenesis by APOBEC cytidine deaminases. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3577.
Abstract 3590: A Neil1 DNA glycosylase germline variant induces genomic instability and cellular transformation
Authors: Sweasy Joann B. , Galick Heather , Kathe Scott , Wallace Susan 
Published: July 2016

Abstract
NEIL1 DNA glycosylase is a bifunctional enzyme that recognizes oxidized pyrimidines and formamidopyrimidines, and appears to remove damage in advance of the replication fork. The rs5745906 SNP of the NEIL1 gene has a minor allele frequency of 1% and is a G to A base substitution that encodes the G83D NEIL1 protein. Interestingly, this mutation is also present in cholangiocarcinomas. Unlike WT NEIL1, the G83D variant is not able to recognize oxidized bases efficiently due to a shift in the void filling residues that stabilize the DNA duplex once a damaged base has been extruded into the glycosylase substrate binding pocket. The goal of our study was to determine if the G83D NEIL1 variant exhibits a cancer-related phenotype in cells. We found that unlike wild-type (WT) NEIL1, expression of G83D in MCF10A immortal human breast epithelial cells induces genomic instability and cellular transformation. Expression of G83D but not WT NEIL1, in MCF10A cells leads to replication fork stalling and slow replication fork velocity. Our results suggest that G83D is unable to remove oxidative DNA damage at the replication fork, resulting in genomic instability and cellular transformation. Our results are consistent with the idea that individuals who harbor the G83D NEIL1 variant are at increased risk for cancer.
Citation Format: Joann B. Sweasy, Heather Galick, Scott Kathe, Susan Wallace. A Neil1 DNA glycosylase germline variant induces genomic instability and cellular transformation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3590.
Abstract 3596: KLLN protects genomic stability by maintaining H3K9 trimethylation (H3K9me3) at the pericentric heterochromatin
Authors: Sankunny Madhav , Nizialek Emily , Niazi Farshad , Eng Charis 
Published: July 2016

Abstract
Dysregulation in the maintenance of chromatin organization resulting in genomic instability is a major driving force for inappropriate development and carcinogenesis. Tumor suppressor genes play a critical role in this regulation through the maintenance of epigenetic marks. Our study focuses on the role of KLLN in the maintenance of pericentric H3K9 trimethylation (H3K9me3) and genomic stability. Germline hypermethylation of KLLN resulting in decreased KLLN expression has been linked to Cowden cancer-predisposition syndrome (CS) in PTEN mutation negative patients. KLLN is a tumor suppressor gene necessary for p53-mediated apoptosis. The protein mediates S-phase arrest and is known to have DNA binding ability. Here, we first used chromatin immunoprecipitation-based sequencing (ChIP-seq) to investigate regions of KLLN binding on the genome and compared it to regions of H3K9me3 enrichment. We used H3K9 specific histone methyltransferase (HMT) activity assay and immunoblotting to measure levels of H3K9me3. Immunostaining was used to study the localization of KLLN, and micronuclei frequency and aberrations in chromosome number was used to assess chromosomal instability. Analysis of ChIP-seq shows enrichment of KLLN binding in regions of H3K9me3. Overexpression of KLLN using plasmid-based transfection correlates with increased H3K9 methyltransferase activity and increased global H3K9me3, while loss of KLLN expression through siRNA-mediated knockdown had an opposite effect. We also established that KLLN localizes to pericentric regions, and loss of KLLN results in dysregulation of pericentric heterochromatin, with consequent chromosomal instability manifested by increased micronuclei frequency and numerical chromosomal aberrations. KLLN regulation of H3K9me3 could be correlated with its interaction with deleted in breast cancer (DBC1). DBC1 is a known inhibitor of SUV39H1, a H3K9 specific histone methyltransferase responsible for maintenance of pericentric heterochromatin. We hypothesize that KLLN sequesters DBC1 through their interaction, thereby abrogating DBC1 inhibition of SUV39H1, resulting in maintenance of pericentric heterochromatin and genomic stability. Our study therefore suggests a critical role for KLLN in the deterrence of tumor initiation and progression.
SIGNIFICANCE: Our study demonstrates a clear role for KLLN in maintenance of chromatin organization thereby maintaining genomic stability, which begins to uncover the basis of KLLN as a tumor suppressor and as a susceptibility gene for inherited cancers.
Citation Format: Madhav Sankunny, Emily Nizialek, Farshad Niazi, Charis Eng. KLLN protects genomic stability by maintaining H3K9 trimethylation (H3K9me3) at the pericentric heterochromatin. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3596.
Abstract 3597: RPS3 regulates melanoma growth and sensitivity to DNA damage and predicts a poor prognosis by targeting ADT3
Authors: Tian Yun , Qin Lijun , Guo Wei , Zhang Changlin , Shi Dingbo , Liu Tianze , Li Wenbing , Wang Jingshu , Li Yixin , Qin Ge , Yu Wendan , Xiao Xiangsheng , Kang Tiebang , Huang Wenlin , Deng Wuguo 
Published: July 2016

Abstract
Melanoma, a malignant skin cancer, is resistant to DNA damage-mediated therapy. Discovering and identifying novel therapeutic targets for melanoma is urgently required. In this study, we found that ribosome protein S3 (RPS3) regulated melanoma growth and the sensitivity of melanoma to DNA damage by targeting ADP/ATP translocase 3 (ADT3). Knockdown of RPS3 inhibited cell proliferation and sensitized melanoma cells to DNA damage. RPS3 knockdown also promoted ADT3 translocation to mitochondrial of melanoma cells when exposed to DNA damage. RPS3 interacted with ADT3 in melanoma cells. Knockdown of ADT3 reduced its co-localization with RPS3. RPS3 could not obviously sensitize melanoma cells to DNA damage with ADT3 knockdown. In addition, we found that Lys18 in the death-induce-domain of RPS3 protein played a critical role in the interaction between RPS3 and ADT3. Mutation at Lys18 site could deadlock ADT3 and attenuate cell apoptosis in melanoma cells. Knockdown of RPS3 also inhibited tumor growth in a melanoma mouse model in vivo, but overexpression of the RPS3-18 mutation rescued the growth. Furthermore, we showed that the patients with higher expressed RPS3 had a much shorter median survival, whereas the patients with higher levels of ADT3 had a much longer median survival. Collectively, our results indicate that RPS3 cooperates with ADT3 to regulate the sensitivity of melanoma to DNA damage and suggest that the RPS3/ADT3 pathway is a potential therapeutic target for human melanoma. Grant support: This work was supported by the funds from the National Natural Science Foundation of China (81472178, 81272195) and the State “973 Program” of China (2014CB542005).
Citation Format: Yun Tian, Lijun Qin, Wei Guo, Changlin Zhang, Dingbo Shi, Tianze Liu, Wenbing Li, Jingshu Wang, Yixin Li, Ge Qin, Wendan Yu, Xiangsheng Xiao, Tiebang Kang, Wenlin Huang, Wuguo Deng. RPS3 regulates melanoma growth and sensitivity to DNA damage and predicts a poor prognosis by targeting ADT3. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3597.
Abstract 360: Detecting intracellular bRAF/cRAF dimerization using a novel luminescent complementation system
Authors: Somberg Richard L. , Schwinn Marie K. , Slater Michael R. , Machleidt Thomas , Cong Mei , Wood Keith V. 
Published: July 2016

Abstract
BRAF mutations can promote constitutive activation of MEK/ERK signaling, leading to unregulated cell proliferation and tumorigenesis. Although inhibitors targeting oncogenic BRAF have shown promise in preventing cell growth, these same inhibitors can paradoxically activate signaling by inducing BRAF interaction with CRAF. Methods for monitoring this undesired outcome are typically low throughput or use kinase binding domains modified with a membrane targeting sequence. We sought to develop a cell-based assay that could reliably detect dimerization of full-length BRAF/CRAF and could potentially be used to rapidly screen inhibitors for modulation of this interaction. To achieve this objective, we utilized a NanoLuc luciferase-based complementation reporter consisting of 1.3 kD (SmBiT) and 18 kD (LgBiT) fusion tags that reconstitute an active luciferase when brought into proximity. In this optimally configured BRAF/CRAF assay, BRAF-LgBiT and CRAF-SmBiT fusions are stably expressed in mammalian cells, and luminescence, indicative of protein interaction, is monitored using a live cell detection reagent. With this assay, we were able to observe rapid and dose-dependent induction of BRAF/CRAF dimerization in response to a panel of kinase inhibitors. The sensitivity and robustness of the assay permitted reliable screening in both 96- and 384-well formats (Z’ factors &gt; 0.9 and 0.6, respectively). Furthermore, the brightness of the reporter allowed the assay to be monitored in individual cells using bioluminescence imaging. These results suggest this BRAF/CRAF complementation assay can enable rapid, high-throughput profiling of kinase inhibitors targeting the RAS/RAF/MEK/ERK signaling pathway.
Citation Format: Richard L. Somberg, Marie K. Schwinn, Michael R. Slater, Thomas Machleidt, Mei Cong, Keith V. Wood. Detecting intracellular bRAF/cRAF dimerization using a novel luminescent complementation system. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 360.
Abstract 3614: Comparison and evaluation of somatic mutation using PGM and proton platform in cell free DNA of non-small cell lung cancer patients
Authors: Sung Jae Sook , Lee Jong Won , Kim Boyeon , Lee Saet Byeol , Kwon Nak-Jung , Lee Won-Chul , Kim Hae Mi , Jang Won Jin , Choi Yun Ji , Park Kyung Hwa , Kim Yeul Hong 
Published: July 2016

Abstract
Non-small cell lung cancers (NSCLC) are characterized by a unique pattern of genetic driver mutations, and some of mutations may be used to predict prognosis and targeted treatment such as EGFR TKIs. Cell free (cfDNA) present in the blood stream shows much potential as a useful cancer maker for early diagnosis and cancer progression monitoring. Especially, analyzing the cfDNA with Next Generation Sequencing (NGS) technology allows high through put examination of various genes concurrently at a low cost. However, there are still no standardized methods to identify mutations in cfDNA. In this study, we examined the viability of PGM and Proton platforms. Ion AmpliSeq Cancer Hotspot Panel v2 (Ion Torrent), covering 2800 COSMIC mutations from 50 cancer genes was used to analyze cfDNA of 125 serum samples from NSCLC patients. The on target was 88% and mean depth was 643x using PGM platform. And, the on target was 92% and mean depth was 22,868x in Proton platform. To validate the results of two NGS platforms, we analyzed EGFR status by sanger sequencing in available 100 tumor tissues. EGFR mutations were identified in 34 (34%) by sanger sequencing. EGFR mutations were identified in 32 (25.6%) and 28 (22.4%) by PGM and Proton platform. Interestingly, out of 34 mutations of tumor tissue, EGFR mutations were matched to 11 and 26 in PGM and Proton platform, respectively. These results showed concordance of 76.5% between the tDNA (sanger sequencing) and cfDNA (Proton). In addition, KRAS (codon 12 and 13) mutations were 4 (3.2%) and 18 (14.4%), respectively. In our study, we demonstrated that Proton platform of high depth is a useful assay to identify somatic mutations of cfDNA in NSCLCs. [This research was supported by the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (HI14C0066)]
Citation Format: Jae Sook Sung, Jong Won Lee, Boyeon Kim, Saet Byeol Lee, Nak-Jung Kwon, Won-Chul Lee, Hae Mi Kim, Won Jin Jang, Yun Ji Choi, Kyung Hwa Park, Yeul Hong Kim. Comparison and evaluation of somatic mutation using PGM and proton platform in cell free DNA of non-small cell lung cancer patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3614.
Abstract 362: A homogeneous bioluminescent succinate assay for detection of jumonjiC domain-containing histone demethylase activities
Authors: Alves Juliano , Goueli Said , Zegzouti Hicham 
Published: July 2016

Abstract
JumonjiC domain-containing histone lysine demethylases (JMJCs) play a pivotal role in determining the epigenetic status of the genome, leading to either transcriptional repression or activation of target genes by counteracting the activities of histone lysine methyltransferases. Because of their implication in cancer, they have become validated drug targets. Therefore, assays for this enzyme subfamily are desirable in order to facilitate the identification of selective and potent inhibitors for drug discovery and as basic research tools. Since succinate is one of the products of the demethylation reaction catalyzed by these enzymes, an assay that detects succinate would be suitable for monitoring all JMJC activities as well as other succinate-forming enzymes (i.e.: dioxygenases). Thus, a bioluminescent and homogenous succinate detection assay for measuring JMJC activity was developed, and it is performed in a two-step format that relies on converting the succinate product to ATP, and then to light in a robust luciferase reaction. The light output is proportional to succinate concentration from low nM to 15μM, and the assay is highly sensitive and robust, two features that are highly desirable and essential for measuring the activity of the majority of JMJC demethylase subfamilies. Therefore, the succinate detection assay is a simple-to-use method that does not require antibodies or modified substrates. Examples of various applications of this succinate detection assay will be presented, including studies on specificity of different substrates by diverse JMJCs, as well as mode of action studies using specific inhibitors. The development of this succinate detection assay will make it possible to investigate a large number of JMJC demethylases and could have significant impact on diverse areas of Epigenetics research.
Citation Format: Juliano Alves, Said Goueli, Hicham Zegzouti. A homogeneous bioluminescent succinate assay for detection of jumonjiC domain-containing histone demethylase activities. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 362.
Abstract 3625: Beyond SNPs: Utilizing NGS methods to detect copy number alterations at high sensitivity in clinical cancer samples
Authors: Raghunath Sharanya , Wayne Jackie , Shamo Aimee , Bradley Patrick , Abanto Moises Hernandez , Loughmiller David , Gillman Jason , Haslem Derrick S. , Stone Gary , Mishra Pravin , Nadauld Lincoln D. 
Published: July 2016

Abstract
The emergence of novel technologies, including Next-Generation Sequencing, has enabled the identification of actionable variants in clinical specimens, which can then be targeted with molecular therapeutics in a precision medicine approach. In human cancers, Single Nucleotide Polymorphisms (SNPs) have become powerful predictors of response to certain targeted therapies. However, Copy Number Alterations (CNAs) also represent a major class of clinically actionable variants that are frequently identified in clinical cancer samples. CNAs account for more than one third of all actionable mutations. A major question in the clinical application of technologies such as NGS is whether CNAs are faithfully detected; a particularly important question given the prevalence of actionable CNAs in cancer samples. To address this question we prepared tumor samples from eleven distinct patients and compared CNA detection on two different NGS platforms. As an orthogonal method for validation, we compared the CNA detection results to Fluorescent In Situ Hybridization (FISH) performed on the same samples. We observed 20 copy number amplification events across the eleven patient samples according to FISH analysis. By comparison, our internal NGS assay, termed ICG100, detected 19/20 (94%) amplification events, whereas an external, commercially available NGS-based test detected only 12/20 (59%) amplification events. Of the seven amplification events that were not identified by the external NGS test, six were considered clinically actionable variants. These findings highlight the discrepancies that exist amongst NGS library preparation chemistries and their abilities to accurately detect CNAs. The relevance of these findings is particularly underscored by the clinically actionable nature of the variants that were discordantly detected, including a high-level ERBB2 amplification.
Citation Format: Sharanya Raghunath, Jackie Wayne, Aimee Shamo, Patrick Bradley, Moises Hernandez Abanto, David Loughmiller, Jason Gillman, Derrick S. Haslem, Gary Stone, Pravin Mishra, Lincoln D. Nadauld. Beyond SNPs: Utilizing NGS methods to detect copy number alterations at high sensitivity in clinical cancer samples. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3625.
Abstract 3627: Automated, purification-free, Ion AmpliSeq™ library preparation from FFPE samples using the Ion Torrent™ Ion Chef™ System
Authors: Biorac Tanya , Allen Michael , Peters Francis B. , Van Loy Cristina , Rhodes Kate , Andersen Mark 
Published: July 2016

Abstract
The ability to produce high quality libraries from FFPE samples is ever more important for next-generation sequencing. Quick turnaround time from sample to answer and simple protocols are critical components for this process. The Ion Chef and Ion AmpliSeq Kit for Chef DL8 is an automated system that has proven to reliably generate quality libraries from purified high molecular weight genomic DNA, in addition to formalin-fixed paraffin embedded (FFPE) DNA samples. We have further developed a simple and robust protocol for preparing DNA libraries from FFPE samples with no nucleic acid purification required. Our protocol is compatible with all Ion AmpliSeq panels and generates eight balanced libraries on the Ion Chef Instrument in under 8 hours, with less than 1 hour hands-on time. We observed equivalent or better sequencing performance using this method compared to a 16-hour manual FFPE DNA extraction protocol. This method has shown to work with low, medium, and high input FFPE samples from different tissue types on a single run. We evaluated a variety of FFPE samples using 1 or 2 pool Ion AmpliSeq DNA research panels containing assays designed to known oncogenes. We were able to generate and successfully sequence DNA libraries from a single FFPE slice as small as 2 mm X 2 mm. Minimal sample handling is an advantage for the NGS platform with this robust protocol.
For Research Use Only. Not for use in diagnostic procedures.
Citation Format: Tanya Biorac, Michael Allen, Francis B. Peters, Cristina Van Loy, Kate Rhodes, Mark Andersen. Automated, purification-free, Ion AmpliSeq™ library preparation from FFPE samples using the Ion Torrent™ Ion Chef™ System. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3627.