bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4888: Clinical sequencing in the National Institute of Health's Clinical Sequencing Exploratory Research (CSER) Program
Authors: Crawford Catherine , Caga-Anan Charlisse , Kaufman Dave , Lee Alexander , Mcewen Jean , Schully Sheri , Hutter Carolyn , Hindorff Lucia 
Published: August 2015

Abstract
To evaluate best uses of and support the integration of genomic sequencing into the clinical workflow, the National Human Genome Research Institute and National Cancer Institute co-fund the Clinical Sequencing Exploratory Research (CSER) project. This initiative aims to 1) leverage NHGRI's experience in genomic sequencing and analysis to facilitate adoption of these methods into patient care, 2) develop and disseminate best practices for the integration of genomic sequencing into clinical care, and 3) research the ethical, legal, and psychosocial (ELSI) implications of bringing broad genomic data into the clinic. The CSER Consortium includes nine multi-disciplinary projects, nine ELSI-specific projects, a Coordinating Center and NHGRI's Intramural ClinSeq program. Four of the multi-disciplinary projects and one ELSI project have a specific focus on cancer settings and outcomes: CanSeq (Dana-Farber Cancer Inst.), BASIC3 (Baylor College of Med.), ONCOSEQ (Univ. of Michigan), and NEXT Medicine (Univ. of Washington) are developing robust frameworks for the integration of whole exome sequencing (WXS) in tumor and germline samples. By measuring the effectiveness of novel platforms for returning results, analyzing the costs and benefits of using sequencing technology to identify rare variants, and evaluating patient experiences, these projects will help define best practices for incorporating WXS into cancer management. As of August 2014, these projects had collected WXS data from 415 patients (269 adults and 146 children). The CSER consortium also has nine working groups that strive to advance best practices and communicate lessons learned to the community regarding the use of genomic sequence data in the clinical workflow. The Tumor Working Group explores the unique technical, interpretive, and ethical challenges involved in clinical sequencing of both somatic and germline cancer genomes. This presentation will highlight progress to date, anticipated products and results, and the relationship between these cancer sequencing projects and broader CSER consortium efforts.
Citation Format: Catherine Crawford, Charlisse Caga-Anan, Dave Kaufman, Alexander Lee, Jean Mcewen, Sheri Schully, Carolyn Hutter, Lucia Hindorff. Clinical sequencing in the National Institute of Health's Clinical Sequencing Exploratory Research (CSER) Program. [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 4888. doi:10.1158/1538-7445.AM2015-4888
Abstract 4893: High-throughput mutation sequencing of the full exon regions in BRCA1 and BRCA2 genes using nanofluidic-PCR prepared libraries
Authors: Wang Jun , Li Guoli , Chen Ming , Heng Jianfu , Guo Xinwu , Peng Limin , Zhang Fan , Li Zibo , Wang Shouman , Xiao Zhi , Dai Lizhong , Yi Wenjun , Tang Lili 
Published: August 2015

Abstract
Breast cancer is one of the most common cancers and also the principal cause of cancer-related death among women in the world. BRCA1 and BRCA2 genes contribute to DNA repair and transcriptional regulation in response to DNA damage. Mutations of BRCA1/2 genes greatly increase lifetime risk to develop breast cancer and these mutations are frequently observed in hereditary breast cancer. In addition, recent studies suggested that breast cancer patients who carry a BRCA1 or BRCA2 germline mutation benefit from poly (ADP-ribose) polymerase (PARP) inhibitors. Therefore, it would be of great interest to develop a high-throughput approach for mutation screening of the full exon regions in BRCA1 and BRCA2 gene.
We have developed a targeted gene exon-sequencing approach using a nanofluidic PCR platform, the Access Array™ system, which enables simultaneous amplification of 48 genetic regions (amplicons) from 48 samples in parallel. We have applied this system to generate the libraries of BRCA1 and BRCA2 coding regions. Total 120 target-specific primer pairs were designed covering all 22 exons of BRCA1 and 26 exons of BRCA2. A primer design strategy was applied to incorporate sample-specific barcodes and Illumina sequencing adaptors into each amplicon, allowing direct sequencing without further library preparation. The exon regions of these 2 genes have been amplified on Access Arrays using 48 multiplex mixes of the 120 primer sets in paired tumor/normal tissues from 144 breast cancer patients. We will present the next-generation sequencing data of BRCA1 and BRCA2 mutation screening collected from amplicon libraries generated using the Access Array system. Our results indicate the excellent utilization of this approach in the mutation screening of BRCA1 and BRCA2 in clinical samples.
Note: This abstract was not presented at the meeting.
Citation Format: Jun Wang, Guoli Li, Ming Chen, Jianfu Heng, Xinwu Guo, Limin Peng, Fan Zhang, Zibo Li, Shouman Wang, Zhi Xiao, Lizhong Dai, Wenjun Yi, Lili Tang. High-throughput mutation sequencing of the full exon regions in BRCA1 and BRCA2 genes using nanofluidic-PCR prepared libraries. [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 4893. doi:10.1158/1538-7445.AM2015-4893
Abstract 4921: Next-generation sequencing as a potential tool in the diagnostics of APC mosaicism in FAP patient
Authors: Yamaguchi Kiyoshi , Komura Mitsuhiro , Yamaguchi Rui , Imoto Seiya , Shimizu Eigo , Kasuya Shinichi , Shibuya Tetsuo , Hatakeyama Seira , Takahashi Norihiko , Ikenoue Tsuneo , Hata Keisuke , Tsurita Giichiro , Shinozaki Masaru , Suzuki Yutaka , Sugano Sumio , Miyano Satoru , Furukawa Yoichi 
Published: August 2015

Abstract
Familial adenomatous polyposis (FAP) is a hereditary disease characterized by the development of multiple adenomatous polyps ranging from hundreds to thousands in the large intestine, and extra-colonic tumors. Patients are predisposed to colorectal cancer that accounts for ∼1% of newly diagnosed colorectal cancer cases. Most of FAP cases result from germline mutations in the tumor suppressor gene APC (adenomatous polyposis coli), but some cases are caused by germline mutations in MUTYH, POLD1, or POLE. The rate of mutation detection depends on the methods used for genetic testing and the genes analyzed in the patients. Although sequence analysis of APC by the Sanger method is routinely performed for genetic testing, there remain cases whose mutations are not detected by the analysis. Next-generation sequencing (NGS) has enabled us to analyze the comprehensive human genome, improving the chance of identifying disease causative variants. In this study, we conducted whole-genome sequencing of a sporadic adenomatous polyposis patient in which we did not find any pathogenic APC mutations by the conventional Sanger sequencing. As a result, whole-genome sequencing and subsequent amplicon-based targeted sequencing identified a mosaic mutation of c.3175G&gt;T, p.E1059X in approximately 12% of his peripheral leucocytes. Additional deep sequencing of his buccal mucosa, hair follicles, non-cancerous mucosa of the stomach and colon disclosed that these tissues harbored the APC mutation at different frequencies. Our data suggest that genetic testing by NGS facilitates the identification of genetic mosaicism responsible for hereditary diseases. NGS will improve genetic diagnosis of hereditary diseases whose mutations have been overlooked by conventional direct sequencing.
Citation Format: Kiyoshi Yamaguchi, Mitsuhiro Komura, Rui Yamaguchi, Seiya Imoto, Eigo Shimizu, Shinichi Kasuya, Tetsuo Shibuya, Seira Hatakeyama, Norihiko Takahashi, Tsuneo Ikenoue, Keisuke Hata, Giichiro Tsurita, Masaru Shinozaki, Yutaka Suzuki, Sumio Sugano, Satoru Miyano, Yoichi Furukawa. Next-generation sequencing as a potential tool in the diagnostics of APC mosaicism in FAP patient. [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 4921. doi:10.1158/1538-7445.AM2015-4921
Abstract 4932: Development of a highly sensitive library prep method for identifying pathogenic variants from FFPE tumor samples
Authors: Young Amanda G. , Lin Charles 
Published: August 2015

Abstract
The application of genomics in cancer has led to an improved understanding of the disease. To date, 125 known driver genes have been discovered*. These genes and their pathways have become the focus of small-molecule drug development. While the number of available targeted therapies is limited, an estimated 800 oncology drugs are in development*, many of which target specific mutations. Single-analyte companion diagnostics exist for the approved therapies, and more might be developed as new therapeutics become available, but the need to assay each variant individually can be ineffective.. An additional, well-known challenge is the degradation and damage caused to DNA in formalin-fixed, paraffin-embedded (FFPE) samples. For these reasons, Illumina is developing a novel method for simultaneous detection of multiple somatic variants from FFPE specimens. This method leverages a multiplexed PCR approach with amplicons designed to a 15-gene panel that can detect somatic variants in 14 genes, and copy number changes in 3 genes. In our experiments, this multiplexed PCR assay has been demonstrated to be highly sensitive, yielding results from as little as 20 ng of DNA extracted from FFPE tissue, even if the DNA is highly damaged and degraded. Somatic variants can be detected down to 5% allele fraction, and gene amplifications can be detected for ≥ 2.2-fold change in copy number. This method, incorporating newly designed software, will be deployed as part of the Illumina Universal Oncology Test System on the MiSeqDx™ (under development), analyzing the sequencing results, and generating reports of mutations and copy number changes in cancer samples.
Citation Format: Amanda G. Young, Charles Lin. Development of a highly sensitive library prep method for identifying pathogenic variants from 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 4932. doi:10.1158/1538-7445.AM2015-4932
Abstract 4936: The interaction and effects of hypoxia, surrounding fibroblasts and p16 expression on breast cancer cell migration and invasion
Authors: Lu Yi , Zhang Jun 
Published: August 2015

Abstract
Cell migration and invasion play essential roles in the metastatic cascade of tumor cells. Accumulated evidences suggest that intratumoral hypoxia, a characteristic of fast-growing solid tumors, promotes cancer cell motile and invasive abilities. In this study, we investigated the effects and interaction of hypoxia, surrounding fibroblasts, and p16 expression on the migration and invasion of breast cancer (BCa) cells MDA-MB-231, JygMC(A) and LM2. We found that hypoxia promoted BCa cell migration and invasion, and cocultured MEF fibroblasts stimulated invasiveness of BCa cells. Moreover, by using a Tet-on inducible system, we found that p16 is capable of inhibiting hypoxia-induced BCa cell migration and invasion (e.g., 36.0% and 85.8% inhibition on migration and invasion, respectively, in MDA-MB-231 cells), and suppressing cocultured fibroblast-stimulated invasiveness of BCa cells. These results suggest that p16, in addition to its well-known anti-tumor proliferation function, has novel anti-cancer properties capable of suppressing hypoxia-mediated cancer cell migration and invasion. This study may provide important validation for p16-mediated cancer therapy either by gene therapy or pharmacological activation of internal p16 gene that is usually inactive due to hypermethylation in the tumor cells.
Note: This abstract was not presented at the meeting.
Citation Format: Yi Lu, Jun Zhang. The interaction and effects of hypoxia, surrounding fibroblasts and p16 expression on breast cancer cell migration and invasion. [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 4936. doi:10.1158/1538-7445.AM2015-4936
Abstract 4965: Multiple ubiquitin-conjugating enzymes modulate the ubiquitination and downregulation of the EGFR by the Cbl RING finger ubiquitin ligase
Authors: Ma Ke , Ryan Philip , Klevit Rachel , Lipkowitz Stanley 
Published: August 2015

Abstract
Receptor tyrosine kinases (RTKs) are known drivers of malignant transformation. Many RTKs (e.g., EGFR, MET) are negatively regulated by ubiquitination and degradation mediated by Cbl proteins, a family of RING finger (RF) ubiquitin ligases (E3s). Loss of Cbl protein function is associated with malignant transformation driven by increased RTK activity. E3s such as the Cbl proteins confer specificity to the ubiquitination process and direct the conjugation of ubiquitin to one or more lysines on the target proteins in collaboration with ubiquitin-conjugating enzymes (E2s). We used enzymatic and yeast two-hybrid assays to characterize the E2s that can interact with Cbl proteins. Using an in vitro E3 assay, we found that only the Ube2d family of E2s mediates autoubiquitination of the Cbl proteins. Subsequently, using the yeast two-hybrid system, we found that Ube2e1, Ube2e2, Ube2e3, Ube2l3, Ube2u, Ube2w and Ube2z can interact with Cbl even though they do not support autoubiquitination of Cbl in the in vitro E3 assay. Among these E2s, three Ube2e family members and Ube2w bind to the RF domain of Cbl as demonstrated by the loss of interaction when the RF domain is disrupted. This suggests that Ube2e and Ube2w are relevant to the ubiquitination and degradation of substrates by Cbl. Knockdown of Ube2w decreases downregulation of EGFR in Hela cells. In the in vitro E3 assay we found that Ube2w can increase autoubiquitination of Cbl mediated by ube2d2. Surprisingly, we found that knockdown of Ube2e increases downregulation and ubiquitination of EGFR in HeLa cells. Mechanistically we found that three Ube2e members inhibit autoubiquitination of Cbl mediated by Ube2d2 in vitro. Further, we showed that Ube2e does not affect ubiquitin charging of Ube2d2 by the ubiquitin-activating enzyme (E1) in vitro. This suggests that Ube2e does not compete with Ube2d2 for the E1 under these conditions. Thus, our data suggest that Ube2e acts as a positive modulator of EGFR signaling by competing for Cbl with Ube2d2 and thus prevents ubiquitination and downregulation of the EGFR by Cbl in combination with Ube2d2. Together these data demonstrate that there is an E2 network which modulates the ubiquitination and downregulation of the EGFR by Cbl.
Citation Format: Ke Ma, Philip Ryan, Rachel Klevit, Stanley Lipkowitz. Multiple ubiquitin-conjugating enzymes modulate the ubiquitination and downregulation of the EGFR by the Cbl RING finger ubiquitin ligase. [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 4965. doi:10.1158/1538-7445.AM2015-4965
Abstract 4982: Increased core fucosylation, a glycan alteration associated with cancer, is the result of hepatocyte dedifferentiation
Authors: Mehta Anand S. , Comunale Mary Ann , Rawat Siddhartha , Garner Jessica , Betesh Lucy , Wang Mengjun , Steel Laura , Bouchard Michael 
Published: August 2015

Abstract
Alterations in N-linked glycosylation have been associated with the development of cancer. One such modification, core fucosylation has been observed in many cancers and is actually used clinically in the diagnosis of hepatocellular carcinoma (HCC). However, the reason why core fucosylation is increased in cancer is unclear. In this study, we show that the activation of specific cancer-associated cellular signaling pathways can increase core fucosylation and induce additional glycoform alterations on hepatocyte proteins. Specifically, we were able to determine that increased levels of protein sialylation and alpha-1,6-linked core fucosylation were observed following activation of the beta catenin pathway. Activation of the AKT pathway or induction of hypoxia also resulted in increased levels of fucosylation and sialylation. Furthermore, we show that increased core fucosylation was directly associated with de-differentiation of hepatocytes and with the transition of cells from an epithelial to a mesenchymal state. In conclusion, we show that increased core fucosylation, a modification of N-linked glycoproteins associated with HCC, occurs as a result of the process of cellular de-differentiation. We believe that this knowledge may help in the use of this glycan modification in the management of those with HCC.
Citation Format: Anand S. Mehta, Mary Ann Comunale, Siddhartha Rawat, Jessica Garner, Lucy Betesh, Mengjun Wang, Laura Steel, Michael Bouchard. Increased core fucosylation, a glycan alteration associated with cancer, is the result of hepatocyte dedifferentiation. [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 4982. doi:10.1158/1538-7445.AM2015-4982
Abstract 4984: EMT and breast cancer metastasis driven by plasma membrane fluidity
Authors: Chang Jeffrey T. 
Published: August 2015

Abstract
New therapeutic targets that can inhibit cancer metastasis are desperately needed. To address this issue, we have leveraged a computational approach and performed an unbiased screen for therapies that can inhibit an epithelial-to-mesenchymal transition (EMT) gene expression profile, a phenotype that is believed to promote metastases. This yielded predictions of drugs that can both promote and inhibit an EMT transcriptional profile. Following up on these predictions, we confirmed that these drugs can induce or repress an EMT in a range of breast cancer cell lines. Furthermore, we discovered that they do so by altering the fluidity of the plasma membrane. An increase in plasma membrane fluidity is necessary and sufficient to induce and maintain an EMT state, increased motility, and increased mammosphere forming ability. Therapies that decrease fluidity can inhibit metastasis in xenograft mouse models. Finally, we found that human cancers can regulate their membrane fluidity through cholesterol homeostasis pathways. 41% of human breast cancers have alterations in cholesterol regulatory pathways, and are associated with a 9 year loss in time to distant metastasis. These data demonstrate that plasma membrane fluidity is a cellular attribute that is leveraged by human tumors to increase metastatic capacity, and that it can, in principle, be targeted by therapeutics to prevent metastasis.
Citation Format: Jeffrey T. Chang. EMT and breast cancer metastasis driven by plasma membrane fluidity. [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 4984. doi:10.1158/1538-7445.AM2015-4984
Abstract 5011: generation of rejuvenated murine antigen-specific T cells by reprogramming to pluripotency and redifferentiation
Authors: Ito Fumito , Fusaki Noemi , Saito Hidehito 
Published: August 2015

Abstract
Background: Adoptive cell therapy with autologous antigen-specific T cells is a promising approach for treating patients with chronic viral infections and various cancers. A major limitation of this approach is the difficulty of obtaining sufficient numbers of T cells with the characteristics necessary for in vivo effectiveness. Less-differentiated T cells with long telomeres would be an ideal T-cell subset for adoptive T cell therapy; however, generating large numbers of these “young” T cells is problematic. This limitation of adoptive T cell therapy can be overcome by using induced pluripotent stem cells (iPSCs) that self-renew, maintain pluripotency, and provide an unlimited source of autologous T cells for immunotherapy. However, in vivo antitumor reactivity of iPSC-rejuvenated T cells remains unknown due to the lack of animal model.
Methods: To establish preclinical model of evaluating iPSC-rejuvenated antigen-specific T cells, we reprogrammed OT-1 T cell receptor (TCR) transgenic CD8 T cells using Sendai virus vectors encoding Oct3/4, Sox2, Klf4 and c-Myc transcription factors. Pluripotency and differentiation capacity of generated iPSCs were evaluated.
Results: Twenty days after infection with Sendai virus vectors, we obtained murine embryonic stem cell-like colonies from OT-1 CD8 T cells. Immunofluorescence staining and RT-PCR analyses revealed pluripotency of established colonies. The iPSCs formed embryoid bodies in vitro, and upregulation of marker genes for all three germ layers was detected. The iPSCs differentiated into teratomas in vivo comprising all three embryonic germ layers in immune-deficient NOD/SCID mice. The iPSCs retained the same rearranged configuration of TCR chain genes as the original OT-1 T cells. Furthermore, OT-1 T cell-derived iPSCs differentiated into T cells on delta-like ligand 1 expressing OP9 (OP9/DL1) murine bone marrow stromal cells.
Conclusions: Generation of rejuvenated T cells by reprogramming to pluripotency and redifferentiation is feasible. This type of approach may be useful for adoptive T cell therapy.
We acknowledge DNAVEC Corporation for kindly providing Sendai virus vectors. This study was supported by the University of Michigan Start-up fund.
Citation Format: Fumito Ito, Noemi Fusaki, Hidehito Saito. generation of rejuvenated murine antigen-specific T cells by reprogramming to pluripotency and redifferentiation. [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 5011. doi:10.1158/1538-7445.AM2015-5011