bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4797: Mutation signature and intratumor heterogeneity of esophageal squamous cell carcinoma in a Chinese cohort
Authors: Song Qingxuan , Liu Mengfei , Bai Jian , Abliz Amir , Yuan Wenqing , Liu Zhen , Liu Jingjing , Zeng Changhong , Cai Hong , Ke Yang , Li Jun 
Published: August 2015

Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common and most aggressive cancers. The epidemiological features of ESCC are extremely complex, with remarkable geographic differentiation among world's populations. While rural Anyang in the Henan Province of China is a well-known high-incidence area, the causal factors in this population remain elusive. We performed exome sequencing of 81 tumor-normal pairs, identified TP53, PIK3CA and NOTCH1 as significantly mutated genes, and observed highly recurrent aberrations in several other genes previously reported for ESCC (ZNF750, MLL2, FAT1, FAT2, and FAT3). Our catalog of ∼7,000 single-nucleotide mutations revealed two main signatures: C&gt;T transitions due to spontaneous deamination of 5-methyl-cytosine, and C&gt;T and C&gt;G mutations at TpCpN attributed to the APOBEC family of cytidine deaminases. Per-sample loadings of these two signatures are uncorrelated with the patient's smoking and drinking status. Since APOBEC activities are associated with exogenous viruses, the prominence of this signature suggests a role of HPV in ESCC etiology, consistent with our previous studies that detected HPV DNA in tumor samples and anti-HPV-E7 antibody in patient's blood. To characterize intratumoral heterogeneity we applied our newly developed method, CHAT, to summarize the clonal frequencies of copy number alternations and single nucleotide mutations in each tumor. Many tumors show a multi-modal distribution of the clonal frequencies, suggesting extensive within-tumor diversity. To better understand the patterns of growth, migration and metastatic potential among different cells within a tumor we performing exome sequencing to compare multiple samples in 10 ESCC patients. For each, we analyzed 4-6 sectors of the tumor, 2-4 samples of adjacent normal tissue, and 1-2 nearby lymph nodes. The spatial heterogeneity of molecular lesions within each tumor is expected to uncover major genes and pathways affected in each patient, as well as the temporal progression of tumorigenic events that may have driven the initiation and outgrowth of ESCC. By integrating the mutation signatures, introtumoral clonal heterogeneity, and clinical outcomes, we aim to gain a better understanding of the molecular bases and evolutionary path of this lethal disease.
Citation Format: Qingxuan Song, Mengfei Liu, Jian Bai, Amir Abliz, Wenqing Yuan, Zhen Liu, Jingjing Liu, Changhong Zeng, Hong Cai, Yang Ke, Jun Li. Mutation signature and intratumor heterogeneity of esophageal squamous cell carcinoma in a Chinese cohort. [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 4797. doi:10.1158/1538-7445.AM2015-4797
Abstract 48: Identification of a novel binding protein playing a critical role in HER2 activation in lung cancer cells
Authors: Ohtsuka Tomoaki , Sakaguchi Masakiyo , Takata Katsuyoshi , Hashida Shinsuke , Watanabe Mototsugu , Suzawa Ken , Maki Yuho , Yamamoto Hiromasa , Soh Junichi , Asano Hiroaki , Tsukuda Kazunori , Miyoshi Shinichiro , Toyooka Shinichi 
Published: August 2015

Abstract
Human epidermal growth factor receptor 2 (HER2) is a member of epidermal growth factor receptor (EGFR) family. Previous studies have revealed that many kinds of malignant tumors have genetic mutations or amplification of HER2, indicating that HER2 alterations are oncogenic. Many kinds of HER2 targeted therapies are effective to HER2 positive tumors, but those treated tumors often get resistance to drugs. Thus, to elucidate HER2 related pathway in cancer biology is important to develop new therapeutic strategy for cancers.
Recently, we newly identified a protein X (a temporary name) as a novel binding protein to HER2 with immunoprecipitation and following LC-Ms/Ms analysis. The protein generally expressed in lung and breast cancers at remarkable level.
We constructed plasmid vectors carrying wild type HER2 and gene X. These vectors were simultaneously introduced to HEK293T cells to examine the binding ability of protein X and HER2 as well as the effect of gene X on HER2-mediated signal-transduction pathway. The approach clearly showed that the expression of gene X, resulted in phosphorylation of HER2 and subsequent activation of oncogenic effector molecules.
We next constructed several kinds of gene X-truncated variants and subjected to the binding assay to look for the binding domain of gene X to HER2. The analysis showed that N-terminal head domain of gene X was essential for the HER2 binding. This domain has an ability to induce HER2 phosphorylation and subsequent activation of the effector kinase, ERK.
In conclusion, we found that gene X is a novel binding protein to HER2 and has a role in HER2 activation.
Citation Format: Tomoaki Ohtsuka, Masakiyo Sakaguchi, Katsuyoshi Takata, Shinsuke Hashida, Mototsugu Watanabe, Ken Suzawa, Yuho Maki, Hiromasa Yamamoto, Junichi Soh, Hiroaki Asano, Kazunori Tsukuda, Shinichiro Miyoshi, Shinichi Toyooka. Identification of a novel binding protein playing a critical role in HER2 activation in lung 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 48. doi:10.1158/1538-7445.AM2015-48
Abstract 4803: BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma
Authors: Harismendy Olivier , Alakus Hakan , Yost Shawn , Woo Brian , French Randall , Lin Grace Y. , Jepsen Kristen , Frazer Kelly A. , Lowy Andrew M. 
Published: August 2015

Abstract
Malignant mesothelioma (MM) arises from mesothelial cells that line the pleural, peritoneal and pericardial surfaces. The majority of MMs are pleural and have been associated with asbestos exposure. Previously, pleural MMs have been genetically characterized by the loss of BAP1 (40-60%) as well as loss of NF2 (75%) and CDKN2A (60%). The rare peritoneal form of MM occurs in ∼10% cases. With only ∼300 cases diagnosed in the US per year, its link to asbestos exposure is not clear and its mutational landscape unknown. We analyzed the somatic mutational landscape of 12 peritoneal MM of epitheloid subtype using copy number analysis (N = 9), whole exome sequencing (N = 7) and targeted sequencing (N = 12). Peritoneal MM display few copy number alterations, with most samples having less than 10 Mbp total changes, mostly through deletions and no high copy number amplification. Chromosome band 3p21 encoding BAP1 is the most recurrently deleted region (5/9), while, in contrast to pleural MM, NF2 and CDKN2A are not affected. We further identified 87 non-silent mutations across 7 sequenced tumors, with a median of 8 mutated genes per tumor, resulting in a very low mutation rate (median 1.3 10-6). BAP1 was the only recurrently mutated gene (N = 3/7). In one additional case, loss of the entire chromosome 3 leaves a non-functional copy of BAP1 carrying a rare nonsense germline variant, thus suggesting a potential genetic predisposition in this patient. Finally, with targeted sequencing of BAP1 in 3 additional cases, we conclude that BAP1 is frequently altered through copy number losses (N = 3/12), mutations (N = 3/12) or both (N = 2/12) sometimes at a sub-clonal level. Our findings suggest a major role for BAP1 in peritoneal MM susceptibility and oncogenesis and indicate important molecular differences to pleural MM as well as potential strategies for therapy and prevention.
Citation Format: Olivier Harismendy, Hakan Alakus, Shawn Yost, Brian Woo, Randall French, Grace Y. Lin, Kristen Jepsen, Kelly A. Frazer, Andrew M. Lowy. BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma. [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 4803. doi:10.1158/1538-7445.AM2015-4803
Abstract 4860: Detection of genetically distinct subclones in cancer: a novel NGS algorithm with high spatial and genetic resolution
Authors: Karagiannis Konstantinos , Chumakov Konstantin , Simonyan Vahan , Mazumder Raja 
Published: August 2015

Abstract
Despite the large number of genome data banks, reference sequences are not always the best match for high-throughput analysis. This is especially true in studies of intratumor heterogeneity where increased mutation rates are observed; the use of a reference genome can complicate the interpretation of the results. Current techniques attempt to circumvent this obstacle by applying de novo assembly algorithms, but the process is slow and often without viable results. Here, we introduce a new technique to decrease the dependency of these pipelines on reference sequences. Our clone discovery algorithm takes advantage of existing alignment data and correlates distant mutations, reported by an alignment algorithm. The algorithm makes no statistical assumption; it extracts information from the overlapping alignments in a step-wise fashion, using reference coordinates of aligned reads. Due to the randomness of noise, the algorithm can be very sensitive and identify clones of low frequency.
Citation Format: Konstantinos Karagiannis, Konstantin Chumakov, Vahan Simonyan, Raja Mazumder. Detection of genetically distinct subclones in cancer: a novel NGS algorithm with high spatial and genetic resolution. [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 4860. doi:10.1158/1538-7445.AM2015-4860
Abstract 487: Whole genome screen to identify genes targeting MYCN-driven embryonal tumors
Authors: Thiele Carol J. , Liu Zhihui , Veschi Veronica , Buehler Eugene , Martin Scott 
Published: August 2015

Abstract
MYCN is a driver of neuroblastoma (NB) tumorigenesis and is over-expressed in a number of tumors of embryonal origin, including rhabdomyosarcoma, medulloblastoma and diffuse intrinsic pontine gliomas. We sought to identify regulators of MYCN transcription by performing a whole genome screen (WGS) for regulators of MYCN promoter activity using a NB cell model. A plasmid containing the MYCN promoter (1.3kb upstream of MYCN TSS) fused to luciferase and stably integrated into the genome of NGP NB cells was the readout system. NGP-MYCNpluc, was selected based on MYCN luciferase activity inhibition by ATRA and HDAC inhibitors to a similar extent as endogenous MYCN mRNA levels. After assay optimization, siRNAs targeting 11,000 genes using 3 siRNAs/gene were evaluated. The siRNA library encompassed the druggable genome and the majority of human transcription factors. Using a 384-well format, siRNAs were reverse transfected in duplicate into NGP-MYCNpluc cells, cultured for 3 days at 37oC and analyzed for luciferase activity and cell viability using a ONE-Glo and Cell Titer-Glo assays (Promega), respectively. A robust statistical measure of median absolute deviation (MAD) was used to standardize siRNA activities in the screen. This identified 36 “high-confidence” genes in which all 3 siRNAs significantly decreased NGP-MYCNpluc luciferase activity, and 49 genes which significantly decrease cell viability. Most drugs associated with the essential viability genes have shown activity in NB cells (bortizamab, gemcitabine/paclitaxel, erlotinib/gemcitabine, UCN-01 and BI 2536). A number of MYCN reporter hits also decreased a CMV luciferase promoter in HEK293 cells, suggesting these hits did not specifically regulate the MYCN promoter. However, several hits did not affect CMV reporter activity, suggesting specificity to the MYCN reporter system. Low-throughput secondary screens are being utilized for assay confirmation and mechanistic evaluation. A 23,000 unique gene set is currently under evaluation and more elegant informatics tools are being used to further illuminate actives within the data
Citation Format: Carol J. Thiele, Zhihui Liu, Veronica Veschi, Eugene Buehler, Scott Martin. Whole genome screen to identify genes targeting MYCN-driven embryonal tumors. [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 487. doi:10.1158/1538-7445.AM2015-487
Abstract 4881: Analysis of long-noncoding RNA interaction at chromatin by chromatin isolation by RNA purification (ChIRP)
Authors: Saito Kan , Taganov Konstantin , Rosenfeld John M. , Asbrock Nick , Chu Vi 
Published: August 2015

Abstract
Gene regulation plays a critical role during development and progression of Cancer. While the regulation of gene expression by transcription factors and epigenetic influences has been well studied over time, pervasive genomic transcription and the role of non-coding RNAs in this process is a rapidly evolving field that remains to be thoroughly explored.
Chromatin Isolation by RNA Purification (ChIRP) is one of the methods, which allows discovery of the sites of interaction of chromatin-associated RNAs (e.g. lncRNAs) with genomic DNA sequences by using probe-based hybridization to target RNA molecules in chromatin. To perform ChIRP multiple biotinylated oligonucleotide probes complementary to the RNA of interest are used. To help eliminate non-specific signals two different pools of probes are used (even and odd probe sets). These probe sets are combined with chromatin and hybridized to the chromatin-associated RNA. Complexes containing biotinylated-probes bound to the chromatin-associated RNA are then isolated using streptavidin magnetic beads. DNA can then be recovered and analyzed by quantitative PCR or next generation sequencing (ChIRP-seq). Alternatively, RNA may also be isolated from an aliquot of the recovered chromatin to detect other RNA molecules that may be associated with the RNA of interest.
To enable the exploration of these RNA interactions in chromatin regulation, we have optimized the methods and developed ChIRP reagents. Using these reagents ChIRP experiments can be performed with reliable recovery of chromatin using lncRNA or other chromatin associated RNA as targets. Additionally, negative and positive control probe sets, and detection primers were developed to ensure first time success. We have performed ChIRP experiments with a HeLa cell lysate and capture oligos for the NEAT1 lncRNA. Isolated DNA was subjected to NGS library construction and sequenced on an Illumina HiSeq™ instrument. Sequences were aligned to the reference genome (hg19). The peaks were called separately for odd and even reactions, and only common peaks were selected. We successfully identified several NEAT1 binding sites in the genomic DNA sequence.
In summary the methods developed allow unbiased discovery of RNA-associated genomic DNA sequences, RNA sequences, and potentially proteins.
Citation Format: Kan Saito, Konstantin Taganov, John M. Rosenfeld, Nick Asbrock, Vi Chu. Analysis of long-noncoding RNA interaction at chromatin by chromatin isolation by RNA purification (ChIRP). [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 4881. doi:10.1158/1538-7445.AM2015-4881
Abstract 4886: Repair of challenging FFPE DNA improves library success rate and sequencing quality
Authors: Liu Pingfang , Chen Lixin , Ettwiller Laurence , Sumner Christine , Stewart Fiona , Dimalanta Eileen , Davis Theodore , Evans Thomas 
Published: August 2015

Abstract
Formalin-fixed, paraffin-embedded (FFPE) clinical samples are an invaluable source of information about genetic alterations in human disease, especially cancer. Next generation sequencing is a powerful tool to mine that information. Unfortunately, sequencing DNA from FFPE samples is challenging due to limited quantities and poor quality, a result of DNA damage incurred during fixation and storage. In this study, we investigated the effects of DNA repair on library preparation and sequencing from FFPE samples. We evaluated a repair enzyme mix that is designed to work on a broad range of DNA damage including modified bases, nicks, gaps, and blocked 3′ ends. Results from FFPE DNA samples of varying quality show that DNA repair generally increases library yields by 10-170%, with the largest improvement on samples of poor quality. Careful analysis of sequencing data shows that base calling qualities for all 4 bases are improved upon DNA repair. Aberrant G:C to A:T mutation were significantly reduced, consistent with cytosine deamination being induced during fixation and storage at room temperature. Interestingly, sequencing miscalls for base pair changes not typically associated with fixation were also reduced. We are currently investigating the source of these mutations. With DNA repair a noticeably positive impact on read mapping and read pairing was observed, resulting in the generation of more useable data. Pretreatment of FFPE DNA by the repair enzyme mix is easily implemented upstream of library construction, allowing fast turnaround time and easy automation. We expect that these improvements will enable the analysis of many FFPE samples that would otherwise not be accessible.
Citation Format: Pingfang Liu, Lixin Chen, Laurence Ettwiller, Christine Sumner, Fiona Stewart, Eileen Dimalanta, Theodore Davis, Thomas Evans. Repair of challenging FFPE DNA improves library success rate and sequencing quality. [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 4886. doi:10.1158/1538-7445.AM2015-4886
Abstract 4887: TCR profiling of T lymphocytes in ovarian tumors and malignant ascites using next-generation sequencing
Authors: Jang Miran , Yew Poh-Yin , Hasegawa Kosei , Ikeda Yuji , Fujiwara Keiichi , Fleming Gini F. , Nakamura Yusuke , Park Jae-Hyun 
Published: August 2015

Abstract
Tumor-infiltrating lymphocytes (TILs) are often observed in many types of solid tumors and considered to reflect the host immune system that eliminates or protects tumor cells. Many studies indicated that higher TIL infiltration is correlated with better prognosis of patients. In addition, some studies suggested that T cells in malignant ascites are associated with clinical outcome. Thus, it is important to define the immune microenvironment in malignant effusions through characterization of T cell repertoire. We here applied a high-throughput next generation sequencing method to characterize T cell receptor (TCR) sequences of a set of primary cancer, ascites, and blood from 12 ovarian cancer patients. We also analyzed the TCR cDNAs of the T cell subtype populations in malignant fluids from 3 ovarian cancer patients. We observed the clonal expansion of certain T cells in tumor and ascites, and found the enriched TCR sequences representing the distinct profiles. Moreover, we investigated TCR sequence signature of CD4+, CD8+, and CD4+CD25+ regulatory T cells in malignant effusion and identified clonally expanded T cell populations. Interestingly TCR sequences among three T cell subsets were almost mutually exclusive. Although the functional studies of clonally expanded T cell populations are definitely required, our approach offers the detailed characterization of T cell immune microenvironment for investigating a beneficial immune response in the host immune system and further contributes to the improvement of cancer immunotherapy.
Citation Format: Miran Jang, Poh-Yin Yew, Kosei Hasegawa, Yuji Ikeda, Keiichi Fujiwara, Gini F. Fleming, Yusuke Nakamura, Jae-Hyun Park. TCR profiling of T lymphocytes in ovarian tumors and malignant ascites using next-generation 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 4887. doi:10.1158/1538-7445.AM2015-4887
Abstract 4897: Accurate variant detection using molecular barcodes
Authors: Cher Charmian , Johansson Henrik , Chi Javelin , Zobeck Katie , Forsmark Linus , Isaksson Magnus , Hogrefe Holly 
Published: August 2015

Abstract
HaloPlex is an amplicon based method for targeted sequencing. The protocol utilizes specificity gained from restriction enzyme recognition, hybridization and DNA ligation to capture molecules originating from the target region to be sequenced. The target region is fully customizable from a single gene up to several thousand discrete regions. Amplicon based methods for multiplex target enrichment are, in general, convenient methods for capturing a wide range of target region sizes. However, in contrast to hybridization capture methods where random shearing is deployed, it is not possible for Haloplex or other amplicon based techniques to use the start point of paired end reads to identify duplicate reads. Duplicate read information can be useful for improving base calling accuracy and to monitor sampling to determine the degree of confidence to assign calls at different presumed allelic fractions. For somatic variants, which are generally present at a lower than 50% allelic fraction, it is even more advantageous to know how many molecules have been sampled when calling a particular base. To enable identification of duplicate reads from libraries prepared with Haloplex, we have added a molecular barcode to the introduced primer cassette. The molecular barcode consists of ten degenerate bases allowing for over one million unique sequences to be present for tagging of molecules. Using information derived from the molecular barcode sequences we demonstrate observation of variants down to 5% allelic fraction in multiple molecules tagged with different molecular barcodes. The new protocol has, besides the introduction of molecular barcodes, been optimized in a few additional aspects. Due to improved reagent formulations and streamlining of workflow, complete target enrichment can now be completed in less than 5 hours. Using 50 ng input we demonstrate &gt;85% specificity and above 90% of target regions being covered at &gt;10% of average depth.
Citation Format: Charmian Cher, Henrik Johansson, Javelin Chi, Katie Zobeck, Linus Forsmark, Magnus Isaksson, Holly Hogrefe. Accurate variant detection using molecular barcodes. [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 4897. doi:10.1158/1538-7445.AM2015-4897