bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4911: Mutually exclusive FGFR2, HER2, and KRAS gene amplifications in gastric cancer revealed by multicolor FISH
Authors: Das Kakoli , Gunasegaran Bavani , Tan Iain Beehuat , Deng Niantao , Lim Kiat Hon , Tan Patrick 
Published: August 2015

Abstract
Gastric cancer (GC) is a major cause of global cancer mortality. Previous genomic studies have reported that several RTK-RAS pathway components are amplified in GC, with individual tumours often amplifying one component and not others (“mutual exclusivity”). Here, we sought to validate these findings for three RTK/RAS components (FGFR2, HER2, KRAS) using fluorescence in situ hybridization (FISH) on a series of gastric tumours, cell lines and patient-derived xenografts. Applying dual-colour FISH on 137 gastric tumours (89 FFPE surgical resections and 48 diagnostic biopsies), we observed FGFR2 amplification in 7.3% and HER2 amplification in 2.2% of GCs. GCs exhibiting FGFR2 amplification were associated with high tumour grade (p = 0.034). In FISH positive tumours, striking differences in copy number levels between cancer cells in the same tumour were observed, suggesting intra-tumour heterogeneity. Using a multicolour FISH assay allowing simultaneous detection of FGFR2, HER2, and KRAS amplifications, we confirmed that these components exhibited a mutually exclusive pattern of gene amplification across patients. The FISH data was also strongly correlated with Q-PCR levels and at the protein level by immunohistochemistry. Our data confirms that RTK/RAS components are mutually exclusively amplified in GC, and demonstrates the feasibility of identifying multiple aneuploidies using a single FISH assay. Application of this assay to GC samples, particularly diagnostic biopsies, may facilitate enrollment of GC patients into clinical trials evaluating RTK/RAS directed therapies. However, the presence of intra-tumour heterogeneity may require multiple biopsy samples to be obtained per patient, before a definitive diagnosis can be attained.
Citation Format: Kakoli Das, Bavani Gunasegaran, Iain Beehuat Tan, Niantao Deng, Kiat Hon Lim, Patrick Tan. Mutually exclusive FGFR2, HER2, and KRAS gene amplifications in gastric cancer revealed by multicolor FISH. [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 4911. doi:10.1158/1538-7445.AM2015-4911
Abstract 4912: Screening of multiplex gene mutations using cell-free DNA in lung cancer patients
Authors: Kwon Nak-Jung , Sung Jae Sook , Seong Ahreum , Kim Hyunmi , Lee Woo Chung , Kim Yeul Hong , Yang Kap-Seok , Seo Jeong-Sun 
Published: August 2015

Abstract
Cell free DNA present in the blood stream shows much potential as a useful cancer maker for early diagnosis and cancer progression monitoring. Especially, analyzing the cell free DNA with Next Generation Sequencing (NGS) technology allows high through put examination of various genes concurrently at a low cost. On average, healthy person's serum contains only about 5ng/ml of cell free DNA, whereas a cancer patient's serum contains up to 1,500ng/ml of cell free DNA. For these reasons, cell free DNA could be a useful cancer marker to further our understanding of the patient's conditions. However, sequencing cell free DNA using NGS platform requires various quality control steps to ensure the quality and the quantity of the cell free DNA extracted and the libraries produced from them.
In this study, we examined the viability of using cell free DNA on NGS platforms. First, DNA was extracted and sequencing libraries were prepared using currently available commercial kits. Next, the quality of the libraries prepared was evaluated through whole genome sequencing on MiSeq. Lastly, lung cancer driver mutation was analyzed using TruSight Cancer Content Set and Ion AmpliSeq Cancer hotspot Panel. Two panels were chosen in order to study the viability of capture hybridization method and amplicon method.
Citation Format: Nak-Jung Kwon, Jae Sook Sung, Ahreum Seong, Hyunmi Kim, Woo Chung Lee, Yeul Hong Kim, Kap-Seok Yang, Jeong-Sun Seo. Screening of multiplex gene mutations using cell-free DNA in lung cancer patients. [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 4912. doi:10.1158/1538-7445.AM2015-4912
Abstract 4922: Analysis of copy number changes in HNSCC by MLPA
Authors: Dalay Nejat , Gurbuz Orkun , Baltaci Elif , Karaman Emin , Buyru Nur 
Published: August 2015

Abstract
Gene amplification is a common finding in a broad spectrum of tumor types, often leading to increased levels of gene expression, a mechanism by which genetic changes contribute to the initiation or progression of cancer. HNSCC is among the neoplasias that frequently show amplification of specific genomic regions. Previous cytogenetic and molecular genetic studies by Fluorescence in situ Hybridization (FISH) and comperative genome hybridization (CGH) and other molecular methods showed that frequently amplified chromosomal regions in primary HNSCC tumors are 3q, 8q, 8p, 11q, 9q. Generally, proto-oncogenes reside in these amplified regions and amplification of these often leads to increased levels of gene expression. Therefore, in this study we investigated amplification of 22 different oncogenes mapping to these regions. The analyses were performed by MLPA on an ABI 3100 genetic analyzer and relative peak areas of the amplification products were evaluated using the Coffalyser MLPA analysis software.
Analysis of 50 HNSCC tumor tissue samples showed that the most frequently amplified genes were from the regions 17q12 (MED1), 11q13.3 (CCND1), 8q (MYC and MTDH) and 8p (ZNF703) with frequencies of 24%, 24%, 20%, 20% and 18%, respectively.
In total, Copy Number Alterations of the CCND1 and MED1 genes were observed in 12 of 50 tumor samples. For the CCND1 gene 6 of these alterations were heterozygous duplications and the remaining 6 were triplications. On the other hand, for the MED1 gene duplications were observed in 8 samples and trriplications were detected in 4 samples. Triplication of the MTDH gene was not observed in any of the amplified samples. However, one third of the ZNF703 amplifications were triplications.
Amplification of the CCND1 and MYC genes are frequently observed in different types of cancers including HNSCC. More recently overexpression of MTDH has been associated with lymph node metastasis and poor-survival in HNSCC. However, to our knowledge there is no data in the literature investigating the ZNF703 gene in HNSCC. Our data indicate that ZNF703 may represent a candidate gene the role of which warrants more detailed analysis in HNSCC.
Citation Format: Nejat Dalay, Orkun Gurbuz, Elif Baltaci, Emin Karaman, Nur Buyru. Analysis of copy number changes in HNSCC by MLPA. [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 4922. doi:10.1158/1538-7445.AM2015-4922
Abstract 4929: An ARMS PCR assay for detection of PI3KCA mutations in FFPE tumor samples
Authors: Yu Dehua Derek 
Published: August 2015

Abstract
The activating mutations of phosphatidylinositol-3-kinase subunit pl10a (PIK3CA) occur in a variety of cancer types and serve as the predictive markers for response to inhibitors targeting a number of receptor tyrosine kinases (RTKs) and PI3K/AKT pathway. Therefore detection of PI3KCA mutations will guide patient selection for effective personalized cancer therapy. Here we reported a new method for the rapid and reliable detection of PI3KCA mutations by using modified mutation-specific ARMS primers.
In this real-time PCR system, the mutant gene is selectively amplified by the modified ARMS primers and the amplicon extending signals are collected by the taqman-probe at the same time.
The ARMS assay could detect 5 mutations on PI3KCA gene with a sensitivity of 0.5% under the background of a total of 10ng wild-type genomic
DNA. By using this assay, we analyzed the PI3KCA mutations in 113 Chinese breast cancer FFPE samples in comparison with Sanger sequencing. Our results indicated that the positive rates were 27.4
%, while 24.8% when measured by Sanger sequencing. The coincidence rates of the two methods were 89.3
% for the positive samples and 96.5% for the negative samples. The total coincidence rate was 97.3%. In conclusion, our study provides a basis for the detection of somatic mutations in PI3KCA in a routine clinical setting. The
ARMS PCR assay allows the detection of the PI3KCA mutations in FFPE samples with better sensitivity and feasibility than the current assays used in clinic.
Note: This abstract was not presented at the meeting.
Citation Format: Dehua Derek Yu. An ARMS PCR assay for detection of PI3KCA mutations in FFPE tumor samples. [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 4929. doi:10.1158/1538-7445.AM2015-4929
Abstract 493: Drug response profiling to inform individualized treatment approaches in high risk leukemia
Authors: Frismantas Viktoras , Rinaldi Anna , Dobay Maria Pamela , Higi Salome , Eugster Sabrina , Marovca Blerim , Horvath Peter , Delorenzi Mauzro , Kunz Joachim , Bandapalli Obul R. , Cario Gunnar , Stanulla Martin , Kulozik Andreas E. , Muckenthaler Martina , Eckert Cornelia , Radimerski Thomas , Bourquin Jean-Pierre , Bornhauser Beat C. 
Published: August 2015

Abstract
Novel treatment approaches are needed for patients with acute lymphoblastic leukemia (ALL) who respond poorly to current therapies. The genotypic diversity identified recently by next generation sequencing technologies within ALL calls for individualized novel strategies. However, functional correlations of oncogenic lesions with drug response profiles are ill defined for ALL. We have established an imaging-based cell viability analysis platform to generate drug response profiles for primary patient-derived ALL samples co-cultured with mesenchymal stroma cells, expecting to derive functional information directly from individual patient samples. Such response profiles may mirror perturbations in relevant cellular programs that could be exploited therapeutically. Our pipeline integrates high-content screening, newly developed bioinformatics tools and biochemical approaches. We screened a library of 65 compounds for activity in 37 precursor B-ALL and 23 T-ALL samples including refractory cases. Cross-sample comparisons revealed that cells from relapsed refractory patients showed a more resistant phenotype for most of the drugs. While only a few agents including genotoxic drugs showed activity across all samples, we detected selective activity of given drugs that distinguish patient sample groups. MLL-rearranged and TCF3-HLF-positive ALL samples as well as a subgroup of T-ALL cases were highly sensitive to the BCL-2 specific BH3-mimetic ABT-199 suggesting BCL-2 dependency for these cases. Multiparametric analyses of in vitro responses predicted in vivo activity of ABT-199 in xenografted mice. Moreover, we could identify synergistic activity of ABT-199 with clinical and preclinical compounds, such as topotecan or epigenetic modifiers. Our drug response profiling pipeline contributes to the identification of distinct vulnerabilities in leukemia and may facilitate the selection of candidate drugs for further development into clinical application.
Citation Format: Viktoras Frismantas, Anna Rinaldi, Maria Pamela Dobay, Salome Higi, Sabrina Eugster, Blerim Marovca, Peter Horvath, Mauzro Delorenzi, Joachim Kunz, Obul R. Bandapalli, Gunnar Cario, Martin Stanulla, Andreas E. Kulozik, Martina Muckenthaler, Cornelia Eckert, Thomas Radimerski, Jean-Pierre Bourquin, Beat C. Bornhauser. Drug response profiling to inform individualized treatment approaches in high risk 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 493. doi:10.1158/1538-7445.AM2015-493
Abstract 4944: Identification of B-cell lymphoma 6 as a novel therapeutic target in glioblastoma
Authors: Chen Ye , Xu Liang , Hazawa Masaharu , Thippeswamy Anand M. , Yang Henry , Müschen Markus , Lin De-Chen , Koeffler Phillip 
Published: August 2015

Abstract
Background
Glioblastoma multiforme (GBM) is one of the most aggressive cancers in humans. Identification and characterization of the GBM-promoting factors is imperative for the development of novel and effective clinical interventions. We recently discovered that the expression of B-cell lymphoma 6 (BCL6), a gene involved in the development of B cell lymphoma, is up-regulated in GBM. This study aims to explore the functional implications of BCL6 in this disease.
Methods
We analysed the transcriptional level of BCL6 in primary glioma samples, and screened the protein expression in a panel of human GBM cell lines as well as primary GBM explants. cDNA microarray analysis was conducted to identify the potential downstream targets of BCL6 in GBM. Small-interfering RNA (siRNA), small hairpin RNA (shRNA), and CRISPR-mediated gene silencing strategies were applied to examine the biological function of BCL6. Finally, inhibitors targeting BCL6 were tested in glioma cells.
Results
In silico analysis revealed elevated BCL6 mRNA levels in both primary GBM samples and cell lines when compared with neural stem cell or non-tumor brain tissues. Western blot confirmed the prevalent expression of BCL6 in GBM cell lines as well as primary GBM explants. Functional studies showed that BCL6 played an important role in promoting cell growth. Depletion of endogenous BCL6 through siRNA, shRNA or CRISPR in GBM cells led to marked inhibition of cell proliferation both in vitro and in vivo.
Transcriptome analysis showed that BCL6 is an important regulator of TP53 signaling pathway. Knockdown of BCL6 increased the expression of p53, p21CIP and p27KIP. CHIP-qPCR further confirmed that BCL6 interacted directly to the TP53 promoter and suppressed its expression.
Moreover, BCL6 negatively regulated MEK-ERK activation in GBM cells. BCL6 depletion reduced the phosphorylation levels of both MEK1/2 and ERK1/2, but had little effect on AKT phosphorylation. Our further investigations uncovered that BCL6 modulated the expression of several key regulators of MEK-ERK pathway, such as SPRY1, SPRY2 and AXL. Finally, BCL6 inhibitor showed marked anti-proliferation activity in GBM cells, suggesting that targeting BCL6 may serve as a new strategy to treat GBM.
Conclusion
Our data suggest that BCL6 is involved in glioma tumorigenesis through regulating both the TP53 and MEK-ERK pathways, and that BCL6 is a potential therapeutic target for glioma treatment.
Citation Format: Ye Chen, Liang Xu, Masaharu Hazawa, Anand M. Thippeswamy, Henry Yang, Markus Müschen, De-Chen Lin, Phillip Koeffler. Identification of B-cell lymphoma 6 as a novel therapeutic target in glioblastoma. [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 4944. doi:10.1158/1538-7445.AM2015-4944
Abstract 4948: The cytosolic domain of a disintergrin and metalloprotease (ADAM) 15 promotes non-small cell lung cancer (NSCLC) proliferation
Authors: Hou Hsin-Han 
Published: August 2015

Abstract
Emerging evidence has indicated that proteins of a disintergrin and metalloprotease (ADAM) family contribute to cancer progression and metastasis. One member of this family, ADAM15, was reported to over-express in multiple cancers, including gastric, lung, breast, and prostate cancers. It has been shown that the enzymatic activities of its extracellular metalloprotease domain mediate ErbB signaling pathway and promote breast cancer proliferation and migration. Nevertheless, in non-small cell lung cancer (NSCLC), the role of ADAM15 and its correlation to patient prognosis is still not well understood. Moreover, unlike in breast cancer, the enzymatic activities of the ADAM15 extracellular domain appeared to be independent of ErbB signaling and lung cancer proliferation, indicating an alternative mechanism of ADAM15 in promoting lung cancer progression. Here, we demonstrated that ADAM15 was over-expressed in primary NSCLC tissues compared to the adjacent normal tissues. Patients with ADAM15 high-expressing lung tumors had shorter survival times. Furthermore, we examined different isoforms of ADAM15 and discovered that, isoform 6 (i6), which contains the most cytoplasmic Src homology 3 (SH3) binding motifs, was significantly upregulated in primary lung cancer tissues. Comparison of i6 and isoform 1 (i1), which has no cytoplasmic SH3 binding motifs, revealed that the cytoplastmic domain is essential for lung cancer proliferation, as well as aggressiveness in an in vitro lung cancer migration model. We also showed that ADAM15 i6, but not i1, mediated ErbB signaling pathway through physical interaction with growth factor receptor-bound protein 2 (Grb2), and activation of Src homolog 2 domain containing (Shc). Most importantly, overexpression of ADAM15 i6 promoted NSCLC cell growth in a xenograft mouse model while knockdown of i6 resulted in tumor shrinkage. Thus, we identified a novel mechanism of the ADAM15 cytoplasmic domain in NSCLC tumor progression, which will not only shed light on the molecular mechanisms of ADAM proteins, but also facilitate development of novel therapy in NSCLC.
Citation Format: Hsin-Han Hou. The cytosolic domain of a disintergrin and metalloprotease (ADAM) 15 promotes non-small cell lung cancer (NSCLC) proliferation. [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 4948. doi:10.1158/1538-7445.AM2015-4948
Abstract 4952: WWOX and LOT1 genes are down-regulated in non-small cell lung cancer (NSCLC)
Authors: Baykara Onur , Ekizoglu Eratak Seda , Kaynak Kamil , Koseoglu Hikmet , Buyru Nur 
Published: August 2015

Abstract
Lung cancer is a result of uncontrolled cell growth in lung tissue and is the most common type of cancer leading to death in men and second after breast cancer in women. Even though smoking is the main reason of lung cancer, genetic and environmental factors play an important role in the onset and prognosis of the disease. The WW domain-containing oxidoreductase (WWOX) gene is a putative tumor suppressor gene located on chromosome 16q23.3-24.1 and is composed of 9 exons. Several studies have reported the role of WWOX gene in different types of carcinomas including lung, breast, ovarian, stomach and nasopharyngeal cancer. The 46kDa WWOX protein has two WW (tryptophan) domains which can recognize and bind the proline-rich region (PPXY) of other proteins. Its main function is to inhibit tumor cell growth. WWOX also plays an important role in wnt/beta-catenin signaling pathway.
The lost-on-transformation 1 (LOT1/ZAC1/PLAGL1) gene is another putative tumor suppressor gene located on chromosome 6q24-25, a common site known for loss of heterozygosity in many tumors. Deletions of the 6q region are observed in different types of cancers including breast, prostate, small cell lung cancer and mesotheliomas. The LOT1 gene codes for a 55 kDa protein with seven C2H2 type zinc finger motifs located in amino terminal half of the protein. This zinc-finger nuclear transcription factor interacts with other proteins and transcription factors exerting antiproliferative effects in cancer cells.
The aim of this study was to investigate the expression levels of the WWOX and LOT1 genes by RT-PCR in tumor tissue samples from 39 patients with non small cell lung cancer (NSCLC). We observed down-regulation of WWOX and LOT1 expression in 82.1% and 48.7% of the patients, respectively. Expression levels of both genes were down-regulated simultaneously in 18 (46.1%) of the patients. When we analyzed the association between gene expression and age, sex, smoking, histology and stage, we found that WWOX expression was decreased in 28 of 31 (90.3%) patients older than 50 years (p = 0.02). Lower expression levels of both genes supports the hypothesis that WWOX and LOT1 act as tumor suppressors in NSCLC and that both genes may have a common effect on tumor progression which warrants further studies to analyze a possible cooperation between the two proteins.
Citation Format: Onur Baykara, Seda Ekizoglu Eratak, Kamil Kaynak, Hikmet Koseoglu, Nur Buyru. WWOX and LOT1 genes are down-regulated in non-small cell lung cancer (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 4952. doi:10.1158/1538-7445.AM2015-4952
Abstract 4955: Somatic alteration and depleted nuclear expression of BAP1 in human esophageal squamous cell carcinomas
Authors: Mori Takahiro , Sumii Makiko , Fujishima Fumiyoshi , Ueno Kazuko , Nagasaki Masao , Ishioka Chikashi , Chiba Natsuko 
Published: August 2015

Abstract
We have found a case of somatic non-synonymous mutation of BAP1, substituting phenylalanine to isoleucine at codon 170 (F170I) out of 49 patients with esophageal squamous cell carcinomas (ESCs) examined by Sanger's direct sequencing. By in vivo Ubiquitination assay, deubiquitininase activity was suppressed in F170I, comparing with wild BAP1. BAP1 localization assay revealed that F170I mutant preferred to localize within cytoplasm although wild BAP1 mostly localizes within nucleus. Microarray analysis revealed that F170I has drastically altered gene expression profile. The following gene-ontology analyses indicated that expression of genes involved in oncogenic pathways has drastically altered by F170I. We have also found that BAP1 expression was depressed around 10% of ESCs examined by immunohistochemistry. It is interesting that nuclear BAP1-depleted cases have strong cytosolic expression of BAP1, instead. As nuclear localization of BAP1 is important in tumor suppressor function, BAP1 may be functionally inactivated around 10% of ESCs.
Citation Format: Takahiro Mori, Makiko Sumii, Fumiyoshi Fujishima, Kazuko Ueno, Masao Nagasaki, Chikashi Ishioka, Natsuko Chiba. Somatic alteration and depleted nuclear expression of BAP1 in human esophageal squamous cell carcinomas. [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 4955. doi:10.1158/1538-7445.AM2015-4955