bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 738: Highly multiplexed and precisely calibrated reference materials for copy number variation detection
Authors: Huang Catherine , Konigshofer Yves , Dickens Jessica , Anekella Bharathi 
Published: July 2017

Abstract
Introduction: Genomic instability is a hallmark of cancer, and copy number variation (CNV), including gene duplication and deletion, can be a key driver of oncogenesis. Detection of CNV is needed for personalized treatment, and may involve microarray analysis or Next Generation Sequencing. Often, DNA from patient-derived cell lines is used as positive control material in these assays. However, these materials are often poorly characterized, may change over time, and have additional confounding genetic alterations. Here we describe the development of new reference materials that are highly characterized by digital PCR and can aid in the validation and calibration of new diagnostic assays for CNV.
Methods: The GM24385 reference cell line has been extensively characterized by the Genome in a Bottle project1 and originates from a participant in the Personal Genome Project. DNA from this cell line was used to make a library of full-length gene inserts. The library had &gt;12X coverage of the GM24385 genome and an average insert size of ~135 Kb. PCR based screening was used to identify and isolate full length MYC, FGFR3 and ERBB2 genes. Next Generation Sequencing, using Illumina Nextera library preparation kits and a MiSeq instrument, was used to verify the gene of interest. The genomic DNA and gene inserts were then formulated into reference materials, in purified DNA format to amplify the copy numbers of these key genes. Digital PCR was used to control the mixing and verify the number of copies of genes and/or mutations within the reference material.
Results: The sequence confirmed genes were formulated into GM24385 genomic DNA at levels consistent with 5X and 10X amplification. Testing on the ArcherDx VariantPlex™ Solid Tumor Kit indicated that each amplification could be detected at the expected level.
Conclusions: Highly characterized and consistently manufactured reference materials for copy number detection are currently lacking. The described Seraseq CNV Reference Materials provide proof of concept for a biosynthetic, engineered material that uses digital PCR as an orthologous reference method and provides a “ground truth” copy number level for key oncogenes.
Citation Format: Catherine Huang, Yves Konigshofer, Jessica Dickens, Bharathi Anekella. Highly multiplexed and precisely calibrated reference materials for copy number variation detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 738. doi:10.1158/1538-7445.AM2017-738
Abstract 739: Orthogonal validation of oncomine cfDNA panel data with digital PCR using TaqMan Rare Mutation Assays
Authors: Venkatesh Vidya , Laig Marion , Varma Kamini , Li Yanchun , Bramlett Kelli , Dhingra Dalia , Chien Richard 
Published: July 2017

Abstract
The discovery of circulating tumor DNA (ctDNA) in the blood, urine and other bodily fluids of cancer patients has led to a new type of non-invasive method of characterizing cancer-causing mutations, the liquid biopsy. With NGS technologies becoming increasingly sensitive, down to a 0.1% Limit of Detection (LOD), they are rapidly gaining traction as a valid assay for cancer genotyping and have potential to direct cancer treatment plans. The wide-angle view provided by NGS panels, combined with dPCR’s zoomed-in precision detection of DNA provide a comprehensive picture of a cancer’s genetic makeup. By applying these complementary techniques at the appropriate time based on the disease type and stage, cancer treatment will become quicker, more precise and more cost-effective in the future. NGS and digital PCR together provide a complete picture of the cancer genome. As part of our research, we wet-lab tested a subset of Rare Mutation Assays corresponding to the Oncomine cfDNA panel for next generation sequencing. Synthetic plasmid (GeneArt) carrying the mutation was spiked into wild-type genomic DNA to reflect a mutation rate of 0.1%. Wild-type genomic DNA was used as negative control. Thermal cycling was performed according to protocol for digital PCR using the QuantStudio 3D. In this study, we tested a pilot set of samples using AcroMetrix Oncology Hotspot Control and Horizon cfDNA Reference Standard with both NGS using Oncomine cfDNA panel and digital PCR with Rare Mutation Assays. Comparison of NGS and digital PCR results for the same sample showed excellent correlation in the low mutation range around 0.1%. This study confirms that digital PCR using QuantStudio 3D and Rare Mutation Assays is effective as a method for orthogonal validation of NGS data using the Oncomine cfDNA panel. Additionally, TaqMan Rare Mutation Assays offer a sensitive and precise solution for downstream mutation tracking over a time course. For Research Use Only. Not for use in diagnostic procedures.
Citation Format: Vidya Venkatesh, Marion Laig, Kamini Varma, Yanchun Li, Kelli Bramlett, Dalia Dhingra, Richard Chien. Orthogonal validation of oncomine cfDNA panel data with digital PCR using TaqMan Rare Mutation Assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 739. doi:10.1158/1538-7445.AM2017-739
Abstract 740: Rapid detection of IDH1/2 mutations using RNaseH2 dependent, multiplex quantitative PCR Assays
Authors: Bao Yun , Baig Aymen , Wang Yu , Iafrate A. John , Chen Caifu , Borger Darrell R. 
Published: July 2017

Abstract
Isocitrate dehydrogenase 1 (IDH1) and 2 (IDH2) are enzymes that normally catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate during glucose metabolism. Heterozygous mutations in the IDH1 and IDH2 genes have been identified in a specific subset of cancers. Mutations typically affect the enzyme active sites at codon R132 in the IDH1 gene, and R140 or R172 in the IDH2 gene. This confers neomorphic enzyme activity that produces the oncometabolite 2-hydroxyglutarate that is involved in cancer initiation and progression. The detection of IDH1/IDH2 mutations has important diagnostic, prognostic, and therapeutic implications and testing for these variants is being incorporated in clinical settings. In fact, the identification of IDH1 or IDH2 gene mutations is now required for the classification of tumors of the central nervous system under the 2016 WHO guidelines. Therefore, there is a significant need for an IDH1 + IDH2 test that can be performed in a rapid manner to support clinical diagnosis and treatment decisions. A strategy utilizing allele-specific quantitative PCR (qPCR) is well suited for evaluating a small number of hotspot variants in IDH1 and IDH2 from clinical tissue samples in a matter of few hours. Using RNase H2-dependent PCR (rhPCR) and a universal reporter system, we have developed new multiplex qPCR assays that effectively discriminate between closely related sequences that differ by only a single nucleotide base at the same position or adjacent position in a single tube reaction. In addition, the rhPCR mechanism of the assays also greatly reduces the impact of primer-primer interactions, further improving the multiplex capability of the assays. During initial testing, specificity, accuracy, and sensitivity were evaluated. Mutations present in patient samples at frequencies as low as 2% were identified with high reproducibility. The assays have been tested across 49 patient samples that included FFPE tissue, blood, and bone marrow aspirate with results that are concordant to those found using an orthogonal method of next generation sequencing. Our study showed that this assay provides a rapid method for detection of multiple IDH1 or IDH2 mutations in single rhPCR reactions with high accuracy, specificity, and sensitivity.
Citation Format: Yun Bao, Aymen Baig, Yu Wang, A. John Iafrate, Caifu Chen, Darrell R. Borger. Rapid detection of IDH1/2 mutations using RNaseH2 dependent, multiplex quantitative PCR Assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 740. doi:10.1158/1538-7445.AM2017-740
Abstract 741: Rapid detection of necrosis in breast cancer with ex vivo and in situ mass spectrometry analysis methods
Authors: Zarrine-Afsar Arash , Shrestha Bindesh , Tata Alessandra , Woolman Michael , Ventura Manuela , Bernards Nicholas , Ganguly Milan , Ginsberg Howard , Zheng Jinzi , Bluemke Emma 
Published: July 2017

Abstract
Necrosis is a form of cell death that is often associated with highly aggressive forms of cancer, is of prognostic value in treatment planning. Mass Spectrometry (MS) is a highly sensitive analytic platform capable of providing a molecular profile of cancer on the basis of mass to charge (m/z) ratio of tissue constituent molecules. MS analysis of ex vivo tissue slices from metastatic murine xenograft tumors from LM2-4 cell line with Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) allowed direct comparisons with histology images to determine the molecular profile of necrotic tissues. The necrotic tissue is characterized by the presence of a ceramide absent from the viable cancer regions. The spatial distribution of this ion fully correlated to necrotic areas from pathology in additional independent tumor samples examined. The same ion was detected from in situ necrotic tissue using tissue aerosols generated by hand-held ablation probes coupled to evaporative ionization interface in only a few seconds of sampling. These developments further establish MS as a novel tool for rapid pathology that is highly complementary to current histology based methods widely used in characterization of cancer in both imaging mode (to provide spatial information on cancer border) and profiling mode (to provide information on cancer type and subtype); all based on unique molecular profile associated with each cancer type and subtype. Current efforts in creating cancer molecular profile libraries will facilitate translation.
Citation Format: Arash Zarrine-Afsar, Bindesh Shrestha, Alessandra Tata, Michael Woolman, Manuela Ventura, Nicholas Bernards, Milan Ganguly, Howard Ginsberg, Jinzi Zheng, Emma Bluemke. Rapid detection of necrosis in breast cancer with ex vivo and in situ mass spectrometry analysis methods [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 741. doi:10.1158/1538-7445.AM2017-741
Abstract 767: Breast cancer in sub-Saharan Africa: a histopathologic review from a tertiary hospital in Northern Nigeria
Authors: Ahmed Saad A. , Kabir Balarabe , Abubakar Nasiru 
Published: July 2017

Abstract
Introduction: Breast cancer is the commonest cancer in women world-wide, however, there are discrepancies in the incidence among different geographical regions. The highest incidence rate is in North American, Northern and Western European, while the lowest rate is found among Asian and sub-Sahara African women. Breast cancer is undoubtedly heterogeneous in terms of its presentation, morphology and molecular profiles. Studies from the developing countries suggested that there are differences between the biology of BC in the developing and developed countries.
Methods: This is a retrospective histopathologic review of breast cancer cases between 1st January 2003 and 31st December 2015 from the Ahmadu Bello University Teaching Hospital Zaria - Nigeria.
Results: A total of 784 breast cancer cases were seen during the study period and majority of the cases (99.4%) were females. The prevalence of breast cancer was found to be 12.6%. Triple-negative breast cancers (TNBC) constitute 67.7% of cases. The mean age was 45.8 ±12.0 years and the youngest patient was 18 years while the oldest was 90 years. Out of the 784 cases, 208 were mastectomies while the remaining were incisional, trucut needle and excisional biopsies. Infiltrating ductal carcinoma NST was the most common histologic variant seen (94.7%) and most of these cases (59.1%) were Grade II tumors. The Nottingham Prognostic Index (NPI) shows that 91.4% of the cases have NPI Score of ≥3.5 with attendant poor 5-year survival rate.
Conclusion: This study found that breast cancer is common and affects mostly women in fifth decade of life. There is a high TNBC among the population studied and therefore androgen receptor profile and genomic studies may be useful to determine the course of therapy.
Note: This abstract was not presented at the meeting.
Citation Format: Saad A. Ahmed, Balarabe Kabir, Nasiru Abubakar. Breast cancer in sub-Saharan Africa: a histopathologic review from a tertiary hospital in Northern Nigeria [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 767. doi:10.1158/1538-7445.AM2017-767
Abstract 790: Regulation of tumor angiogenesis by low dose Aspirin
Authors: Chakraborty Jinia , Maity Gargi , Banerjee Snigdha , Banerjee Sushanta K. 
Published: July 2017

Abstract
Background and Objective: Tumor angiogenesis is a pathophysiological process in which new blood vessels are formed in the primary tumor site or distant organs for the nourishment of cancer cells and metastatic growth. Thereby, targeting tumor angiogenesis is an important area of research for cancer therapy. Abnormal structure of blood vessels (i.e. leakiness due to abnormal lining of pericytes on the microvessels) is one of the critical features of tumor angiogenesis that sensitizes vascular cells to cytokines and helps circulating tumor cells to metastasize to distant organs. Our long term goal is to repurpose the drugs that may prevent tumor angiogenesis or normalize the vessels by repairing leakiness via recruiting pericytes or both. Our recent studies found that Aspirin (ASA) has the potency to inhibit breast cancer growth and metastasis, as well as reprogram the mesenchymal to epithelial transition (MET). Given the importance of ASA, we tested whether ASA may be able to regulate tumor angiogenesis.
Methods: To do so, we determined the effect of low dose ASA (1mM, which is equivalent to 80mg human dose), ASA-treated (2.5mM) conditioned media (231-CMASA) or vehicle-treated conditioned media (231-CMVT) of MDA-MB-231 cells on different endothelial cell physiology. These include endothelial cells’ migration towards serum using 3D modified Boyden chamber assay, in vitro capillary-like structure formation on Matrigel, cell permeability using in vitro endothelial permeability assay and interactions of pericytes-endothelial cells. We also determined the effect of ASA on various angiogenic factors associated with tumor angiogenesis. Finally, we determined the effect of ASA on in vivo tumor angiogenesis using in vivo Angiogenesis Assay (Trevigen)
Results and Conclusions: We found that 231-CMASA significantly blocks in vitro migration, the formation of in vitro capillary-like structures parallel with leakiness via incomplete interaction of pericytes and endothelial cells as compared to 231-CMASA. The antiangiogenic effect of ASA was also documented in in vivo assays. Mechanistically, ASA treatment blocks several angiogenic factors including VEGF-A that are associated with these three events, implicating a low dose of Aspirin is potentially therapeutic for breast cancer via blocking and normalizing tumor angiogenesis.
Citation Format: Jinia Chakraborty, Gargi Maity, Snigdha Banerjee, Sushanta K. Banerjee. Regulation of tumor angiogenesis by low dose Aspirin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 790. doi:10.1158/1538-7445.AM2017-790
Abstract 797: Glioblastoma animal model using CRISPR-Cas9 technology
Authors: Jeong Da Eun , Lee Kee Hang , Kim Sung Soo , Bae Yoon Kyung , Nam Hyun , Hwang Ji Yoon , Pyeon Hee Jang , Song Hye Jin , Joo Kyeung Min 
Published: July 2017

Abstract
Current in vivo model system poses limitation on fully recapitulating genomic characteristics of a tumor due to high complexity and poor understanding of the heterogeneous microenvironment conditions in cancer pathogenesis. In an effort to address such issues, strategic models are required. In present study, we propose that the most representative cancer models have consistent tumor microenvironments and genomic mutations. The Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system is a powerful genome editing tool for efficient and precise genome engineering. Here, we employed CRISPR-Cas9 system in vivo to generate Cre-dependent Cas9 knock-in mouse (B6;129-Gt(ROSA)26Sortm1(CAG-cas9*,-EGFP)Fezh/J, Jackson lab.). The Cre-dependent Cas9 mouse models harbor combinations of genomic alterations including well-established oncogenes such as EGFRviii, c-MET, PDGFRa, IDH1 R132H and KRAS, EGFR, ALK, BRAF in Brain and Lung cancer models, respectively. While, they also consist of tumor suppressor genes including PTEN, NF1, Ink4a/ARF, Rb, TP53 and TP53, PTEN, NKx-1, APC in both Brain and Lung models, respectively. Cre-dependent model allows us to study in-depth into the tumor initiation and progression, while able to follow up in the role of tumor microenvironment in cancer maintenance. A better understanding of cancer models for preclinical research including their uses, as well as their limitations, may aid future potential studies regarding the development and implementation of new immune targeted therapies and potential validation of novel therapeutic biomarkers.
Citation Format: Da Eun Jeong, Kee Hang Lee, Sung Soo Kim, Yoon Kyung Bae, Hyun Nam, Ji Yoon Hwang, Hee Jang Pyeon, Hye Jin Song, Kyeung Min Joo. Glioblastoma animal model using CRISPR-Cas9 technology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 797. doi:10.1158/1538-7445.AM2017-797
Abstract 803: Targeting β-catenin/CBP signaling in OSCC
Authors: Alamoud Khalid , Sadykov Khikmet , Kartha Vinay , Monti Stefano , Belkina Anna , Snyder-Cappione Jennifer , Pai Sara , Kukuruzinska Maria 
Published: July 2017

Abstract
Objectives: Oral squamous cell carcinoma (OSCC) is an aggressive malignancy characterized by molecular heterogeneity and locoregional spread associated with high morbidity. Aggressive cancers are thought to arise from populations of cancer initiating cells (CICs) that exhibit the properties of stem cells and drive tumor development, recurrence and resistance to therapy. The transcriptional regulator, β-catenin, has been implicated in OSCC CICs. Nuclear β-catenin has been shown to recruit the chromatin remodeling CREB binding protein (CBP) to drive expression of proliferation and survival genes, as well as genes that maintain stem-like phenotypes. We hypothesized that targeting β-catenin-CBP interaction will inhibit CICs in oral tumors and restore an epithelial phenotype.
Methods: To test tumor aggressive potential of OSCC CICs, we used zebrafish as a model system. We isolated CD44+CD24hiCD29hi cells fom aggressive HSC-3 OSCC cells by FACS and assayed their ability to drive tumor growth and metastases in zebrafish compared to unsorted and CD44+CD24lowCD29low cells. In addition, we examined the role of the β-catenin/CBP axis in the aggressive phenotype of these cells. We also assessed whether the β-catenin/CBP axis affected CICs in tumors from immune competent HPV+ mice.
Results: Zebrafish injected with subpopulation of cells co-expressing CD44+CD24hiCD2hi primitive cell surface markers drove rapid tumor growth and metastases, followed by unsorted and sorted CD44+CD24lowCD29low. Treatment of CD44+CD24hiCD29hi cells with a small molecule inhibitor of the β-catenin-CBP interaction, ICG-001, interfered with tumor growth and metastases in zebrafish. Further, ICG-001 inhibited tumor growth in immunocompetent HPV+ murine model. On a cellular level, ICG-001 promoted membrane localization of β-catenin, enhanced E-cadherin adhesion and restored epithelial phenotype. Significantly, ICG-001 gene signatures tracked with reduced overall patient survival in the cancer genome atlas, TCGA. Conclusion: Our studies indicate that the β-catenin/CBP axis promotes OSCC CICs and that ICG-001 may be an effective therapeutic agent for this malignancy.
Support: Evans Center for Interdisciplinary Biomedical Research ARC funding AU 5303015 8000000.
Citation Format: Khalid Alamoud, Khikmet Sadykov, Vinay Kartha, Stefano Monti, Anna Belkina, Jennifer Snyder-Cappione, Sara Pai, Maria Kukuruzinska. Targeting β-catenin/CBP signaling in OSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 803. doi:10.1158/1538-7445.AM2017-803
Abstract 805: KRASG12D and TP53R167H cooperate to induce pancreatic carcinoma in conditional transgenic Sus scrofta
Authors: Principe Daniel , Overgaard Nana , Diaz Andrew , Torres Carolina , McKinney Ronald , Dawson David , Rund Laurie , Schwind Regina , Grippo Paul J. , Schook Lawrence 
Published: July 2017

Abstract
Although survival has improved in recent years, pancreatic ductal adenocarcinoma (PDAC) remains remarkably virulent with a median survival time of only four months. As there is no effective strategy for the management of PDAC, there is a need for the development of new preclinical strategies. The majority of this work is being done in genetically modified mice, which faithfully recapitulate a variety of pancreatic cancer histotypes. While mice have allowed for unprecedented insight into pancreatic cancer etiology, due to fundamental differences in anatomy and physiology, mouse models of PDAC often fail to accurately predict responsiveness to therapy. As the pig pancreas has more similar anatomical orientation and localization to humans than that of rodents, pigs may serve as a more relevant model for PDAC and other malignancies of the pancreas. As KRAS and TP53 mutations are observed in approximately 95% and 70% of PDAC patients, respectively, we generated Cre/lox transgenic Sus scrofta expressing a LSL-KRASG12D-TP53R167H cassette and administered an Adeno-Cre particle to the pancreas gland parenchyma. This resulted in a mixed histoype of metastatic leiomysarcoma and neoplastic disease of the pancreas. To produce a similar pancreas histoype while avoiding the leiomyosarcoma, we next restricted the Adeno-Cre administration to the main pancreatic duct, which resulted in both PDAC and neuroendocrine carcinoma with no abnormality of the smooth muscle. This serves as the first large animal model of pancreatic carcinogenesis, and given the anatomical/physiological similarity of pigs and humans, may allow for insight into new avenues of research not before possible in rodents.
Citation Format: Daniel Principe, Nana Overgaard, Andrew Diaz, Carolina Torres, Ronald McKinney, David Dawson, Laurie Rund, Regina Schwind, Paul J. Grippo, Lawrence Schook. KRASG12D and TP53R167H cooperate to induce pancreatic carcinoma in conditional transgenic Sus scrofta [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 805. doi:10.1158/1538-7445.AM2017-805