bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2113: The effects of enzymatic digestion on epitope detection by flow cytometry
Authors: Middlebrook Aaron J. , Austin Caitlin , Santos Daniel , Snowden Eileen , Porter Warren , Hahn Friedrich , Ferguson Mitchell , Blaesius Rainer , Ghanekar Smita
Published: August 2018

The heterogeneous nature of solid tumors, coupled with the relatively small sample size of available biopsies, has led to an emerging need to glean as much information as possible from these valuable specimens. Current approaches to solid tumor analysis fail to completely reveal the diverse range of cellular compartments that comprise the tumor microenvironment. A comprehensive approach to tumor interrogation requires efficient tissue dissociation to facilitate analysis at the single-cell level. In contrast to current methods, single-cell analysis of tumor derived cell suspensions by flow cytometry has the potential to provide a more complete understanding of the many subpopulations within the tumor microenvironment and the cell to cell interactions that govern this space. In order to prepare a cell suspension from solid tumor tissue, most investigators subject the tumor sample to a combination of mechanical and enzymatic dissociation modalities. Regardless of the combination of enzymes used for dissociation, there exists a degree of non-specific proteolytic cleavage. In the work presented here, we set out to quantify the non-specific cleavage associated with a proprietary enzyme mixture developed for tumor dissociation. Using a mixed sample that included peripheral blood mononuclear cells and several cell lines, we were able to generate a sample that expressed approximately 90% of our current antibody catalog. By staining our sample with a rudimentary 3 color panel, we were able to identify 10 individual cell populations based on marker expression and/or scatter. This composite sample was left untreated or exposed to our propriety mixture of dissociation enzymes and then subsequently screened for all 251 antigens in our catalog. The impact of non-specific proteolytic cleavage on surface marker detection was gauged in terms of median fluorescence intensity of positive population and stain index. Our results indicate that of the 251 surface markers tested in our experimental series, less than 10 percent were significantly affected by enzymatic digestion. Of those markers that were affected only a fraction of them were affected to such an extent that it was impossible to detect positive expression. These results underscore the importance of understanding the factors that can influence surface marker detection and bolster our confidence that this particular mixture of enzymes is imparting minimal impact on surface marker detection.

Citation Format: Aaron J. Middlebrook, Caitlin Austin, Daniel Santos, Eileen Snowden, Warren Porter, Friedrich Hahn, Mitchell Ferguson, Rainer Blaesius, Smita Ghanekar. The effects of enzymatic digestion on epitope detection by flow cytometry [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2113.
Abstract 2128: Autocrine fibronectin inhibits breast cancer metastasis
Authors: Shinde Aparna , Abdullah Ammara , Solorio Luis , Wendt Michael
Published: August 2018

The processes of the epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) are strongly linked to breast cancer metastasis via their ability to generate cells of increased invasive capacity and enhanced tumor-initiating phenotypes. Numerous growth factors, cytokines and chemotherapies present in the tumor microenvironment are capable of inducing EMT, but the role of extracellular matrix (ECM) components in this process remains less well understood. Analysis of the METABRIC dataset strongly linked high-level FN expression to decreased patient survival. However, in vitro analysis of the MCF-10A progression series indicated that autocrine FN expression was associated with nonmetastatic cells. Therefore, we utilized differential bioluminescent imaging to track the metastasis of these isogenic epithelial and mesenchymal cells within heterogeneous primary tumors. Using this approach, we demonstrate that tumor cells expressing autocrine FN display a constitutively mesenchymal phenotype and are incapable of completing the metastatic process, even when grown within a tumor containing epithelial tumor cells. Importantly, depletion of FN allows tumor cells to exit their mesenchymal state, regain epithelial characteristics and initiate tumor growth in a metastatic microenvironment. Using a tessellated three-dimensional polymer scaffolding, we show that depletion of FN or pharmacologic inhibition of focal adhesion kinase prevents mesenchymal tumor cells from producing structural fibrils and thus supporting the growth and migration of metastatic-competent epithelial tumor cells. Finally, dynamic FN coating of this 3D growth scaffold resulted in formation of a functionalized fibrillar FN network that was sufficient to induce transient EMT events as metastatic cells migrated along FN fibrils. Taken together, our data indicate that autocrine expression of FN by tumor cells supports a stable mesenchymal phenotype limiting their metastatic potential. Instead, this tumor cell-derived production of fibrillar FN acts in a paracrine fashion to support transient EMT events in metastatic competent cells within a heterogeneous tumor microenvironment.

Citation Format: Aparna Shinde, Ammara Abdullah, Luis Solorio, Michael Wendt. Autocrine fibronectin inhibits breast cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2128.
Abstract 2159: Use of in vitro cell sheet engineering as a chemotherapeutic model for epithelial cancer
Authors: Kim Eun Hye , Lee Jaewang , Shin Daiha , Park Sunwoo , Kwon Minsu , Roh Jong-Lyel
Published: August 2018

Epithelial cancer is grown in the in vivo microenvironment mixed of keratinocytes, fibroblasts and matrix, vessels, and immune cells. The current in vitro 2-dimensional (2D) models for anti-cancer drug testing are commonly performed on a physical basis, resulting in significant difference from elucidating the real in vivo effects. To resolve the experimental gap, the 3D models have been developed to mimic the in vivo cancer microenvironment, while there is a lack of specific models for epithelial origin tumors. Therefore, we developed a new 3D model of using the in vitro cell sheet engineering for epithelial cancers and compared the results of several chemotherapeutic drug testing among in the 3D model, spheroid culture, and 2D-dish cell culture. The cell sheet included epithelial and subepithelial layers consisting of keratinocytes overlying the mixture of fibroblasts and endothelial progenitors. The spheroids of green fluorescent protein-tagged epithelial cancers were placed at the interface of epithelial and subepithelial layers. The spheroids with mixture of cancers and fibroblasts or cancer-associated fibroblasts (CAF) were made by the conventional hanging-drop method, and the 2D was simply seeded in the culture dish. The cell growth, viability, and hypoxia were calculated by cell counting kit (CCK), live/dead assay, propidium iodide and LOX-1 staining. The morphology, invasion, and mRNA and protein expressions were also compared among the different in vitro models. The results of live/dead assay and CCK showed higher viabilities in the cell sheet-based models before and after treatment with chemotherapeutic drugs. TGF-β and epithelial-mesenchymal transition-related mRNA and proteins were highly expressed in tumors growing in the cell sheet. Further, the incorporation of CAF into the cancer spheroids appeared to less decrease viable cancer cells by chemotherapeutic agents compared to the use of no or normal fibroblasts. Tumor angiogenesis and hypoxia were also apparently observed in the cell sheet model, which partly contributed to relative resistance to chemotherapeutic drugs. Taken together, the cell sheet-based cancer model might be applied to the in vitro observation of epithelial cancer growth and invasion, and anti-cancer drug testing.

Citation Format: Eun Hye Kim, Jaewang Lee, Daiha Shin, Sunwoo Park, Minsu Kwon, Jong-Lyel Roh. Use of in vitro cell sheet engineering as a chemotherapeutic model for epithelial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2159.
Abstract 2164: Conditional tumor cell reprogramming: From in vitro sensitivity to in vivo PDX modeling
Authors: Long Yuan , Van Loc , Xi Song , Li Le , Zheng Yuhui , Ling Ying , Zhang Feifei , Cheng Jijun , Wen Danyi
Published: August 2018

Tumor cell immortalization through conditional reprogramming, particularly from limited biopsy specimen, is an invaluable tool to generate propagating tumor cells for cell-based diagnostics, drug sensitivity assay and bio-banking in vitro. We have successfully reprogrammed primary tumor cells from a number of unreported tumor types, including lung carcinoma and adenoid cystic carcinoma, towards immortalization. The propagating cells exhibited typical colonized growth, which is well maintained upon cryo-frozen. In some cases, the cells can be passaged for multiple times and likely become useful cell lines. Like primary tumor cells, conditional reprogrammed tumor cells are reliable to test drug sensitivity in vitro. We attempt to extend conditional reprogrammed tumor cells to reconstitute and grow PDX models in vivo for testing drug efficacy. Preliminary data indicate that, in a 7-day in vivo assay utilizing hollow-fiber tubes grown subcutaneously in mouse, which we call OncoVee Mini-PDX, conditional reprogrammed tumor cells, like primary tumor cells and PDX tumor cells, can be successfully used to test drug efficacy in vivo. In summary, this study explores and evaluates applications of conditional reprogrammed tumor cells in drug efficacy tests both in vitro and in vivo.

Citation Format: Yuan Long, Loc Van, Song Xi, Le Li, Yuhui Zheng, Ying Ling, Feifei Zhang, Jijun Cheng, Danyi Wen. Conditional tumor cell reprogramming: From in vitro sensitivity to in vivo PDX modeling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2164.
Abstract 2166: Dasatinib displays antitumor efficacy in an orthotopic xenograft mouse model of histiocytic sarcoma
Authors: Takada Marilia , Smyth Lauren , Yuzbasiyan-Gurkan Vilma
Published: August 2018

Histiocytic sarcoma (HS) is an orphan hematological malignancy with an incidence of less than 1% of all non-Hodgkin's lymphoma, affecting both children and adults. It is a highly metastatic disease, and can affect any organ in the body including spleen, lungs, bone marrow, liver and lymph nodes. It is associated with a poor prognosis as treatment options are scarce and responses are short lived. Dogs spontaneously develop a similar form of HS with an appreciable frequency, and therefore present a unique translational model to investigate better treatments. Preliminary data from in vitro studies identified dasatinib, a multi tyrosine kinase inhibitor, as a highly potent drug against HS cell lines derived from tumors in dogs, but non-toxic to normal normal tissue surrogate fibroblasts. The current study was undertaken to evaluate if the efficacy of dasatinib could be re-capitulated in an in vivo orthotopic xenograft model of HS. The mouse model was generated in NOD-SCID mice by surgical injection of HS cells, transfected with a luciferase reporter construct, into their spleen. Tumor growth was monitored using In Vivo Imaging System. Mice were treated with 30 mg/kg of dasatinib intraperitoneally once a day or vehicle control, with five mice in each group. Dasatinib treated mice had a significantly decreased tumor growth rate in comparison to untreated mice. Most importantly, treatment with dasatinib significantly increased their survival time. All mice from the vehicle control group reached humane endpoints for euthanasia by day 27, while treated mice were clinically stable at day 53, with the difference in survival being highly significant (p<0.0001). In conclusion, here we report the first orthotopic xenograft mouse model of HS, that offers the possibility to test therapeutic response to novel agents, such as dasatinib. Our findings indicate that dasatinib is a promising treatment option for HS, and provide a rational for the initiation of clinical trials.

Citation Format: Marilia Takada, Lauren Smyth, Vilma Yuzbasiyan-Gurkan. Dasatinib displays antitumor efficacy in an orthotopic xenograft mouse model of histiocytic sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2166.
Abstract 2182: DigiPico: A whole-genome sequencing approach to investigate microscopic residual chemotherapy resistance disease in ovarian cancer
Authors: KaramiNejadRanjbar Mohammad , Fotso Donatien Chedom , Zheng Yuhao , Yau Christopher , Ahmed Ahmed
Published: August 2018

Microscopic residual chemotherapy resistance disease (MRCD) following cancer therapy predisposes to recurrence. Genome analysis of MRCDs could, therefore, give insights into evolutionary mechanisms that might govern this process. However, to date, this has largely been restricted to studies utilizing targeted sequencing of known somatic mutations due to the challenges of whole-genome sequencing of subnanogram quantities of DNA. A previous report showed that obtaining accurate whole-genome sequencing is possible from as little as 10 to 20 cells with the added advantage of obtaining reconstructed long fragment reads. Adopting this technology, we were able to optimize a procedure to accurately obtain high-quality whole-genome sequencing data from minimally available clinical samples such as MRCDs, termed DigiPico. Using DigiPico, we were able to perform sequencing on several post-chemotherapy MRCDs and single tumor islets from a high-grade serous ovarian cancer (HGSOC) tumor. The data were found to be highly accurate, with over 96% of the single-nucleotide polymorphisms (SNPs) being detected in DigiPico sequencing results despite the extremely low amount of material available. Moreover, we found that DigiPico can be used for calculation of allele fractions with a consistency rate of up to 84% as opposed to a consistency rate of only 47% for when a standard multiple displacement amplification of similar amount of DNA is used during library preparation. The high-quality allele fraction information from DigiPico was then used to predict the copy number variation (CNV) in these clinical samples. Here, we showed the power of DigiPico for accurate SNP calling and CNV prediction from post-chemotherapy MRCDs and single tumur islets of a HGSOC tumor, the latter of which is extremely important for studying HGSOC as these tumors often show a great degree of structural alterations. This information can now be used for better understanding of how MRCDs might be able to remain unharmed during the course of chemotherapy and initiate recurrence after completion of treatment, which in turn can allow us to design better treatment strategies for HGSOC patients.

Citation Format: Mohammad KaramiNejadRanjbar, Donatien Chedom Fotso, Yuhao Zheng, Christopher Yau, Ahmed Ahmed. DigiPico: A whole-genome sequencing approach to investigate microscopic residual chemotherapy resistance disease in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2182.
Abstract 2187: A rapid autopsy program for cancer research
Authors: Beach Thomas G. , Sue Lucia I. , Serrano Geidy E. , Intorcia Anthony , Walker Jessica , Glass Michael , Callan Michael
Published: August 2018

Many new technologies, such as genomics, transcriptomics, proteomics and metabolomics, are directed at molecular-level analyses of high-quality human normal and diseased tissues. At present, however, the relative lack of suitable tissue for this work is a critical roadblock to the full utilization of these new methods. Tissue is traditionally collected at the time of therapeutic surgical interventions, such as biopsy, or at the time of death, by autopsy. Biopsy is only done on individuals with disease and therefore normal control tissues are only obtained by chance. Biopsy tissue is often completely used for diagnostic purposes or is insufficient in quantity to constitute a shared resource, or for studies of intra-tumoral heterogeneity. Metastatic tissue is often not biopsied, precluding analysis of its evolving molecular changes. Both diseased and normal control tissue could potentially be obtained at autopsy, but autopsy tissue is generally only suitable when it is rapidly obtained after death. The Brain and Body Donation Program (BBDP) in Sun City, Arizona, is a not-for-profit longitudinal clinicopathological study of aging and is the world's only consistently-rapid autopsy program (3 h median). Board-certified pathologists diagnose all tissue microscopically. Many cases have both primary and metastatic tumor tissue. Both fresh-frozen & formalin-fixed samples are saved. All subjects are research volunteers with comprehensive clinical documentation. Our informed consent allows wide sharing of tissue and data, including with for-profit companies. More than 100 cancer autopsies have been done; fixed and frozen tissue is available from more than 25 cancer types, many of which have both primary and metastatic tumor tissue. Normal control tissue is available from more than 40 tissue types and RNA quality is high (Walker DG et al, Cell Tissue Bank 2016 17(3):361-75). The BBDP is listed on the NCI Specimen Resource Locator, and inquiries may be made directly to our website, www.brainandbodydonationprogram.org.

Citation Format: Thomas G. Beach, Lucia I. Sue, Geidy E. Serrano, Anthony Intorcia, Jessica Walker, Michael Glass, Michael Callan. A rapid autopsy program for cancer research [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2187.
Abstract 2192: Single-molecule single-cell DNA sequencing identifies ongoing copy number evolution in BRCA breast cancers
Authors: Du Haowei , Davis Alexander , Gao Ruli , Colic Medina , Sei Emi , Hu Min , Barrera Angelica Gutierrez , Casasent Anna , Albarracin Constance , Arun Banu , Navin Nicholas E.
Published: August 2018

BRCA2 germline mutation carriers have a lifetime risk of 72% for developing invasive breast cancer. Although BRCA2 has been implicated in double-stranded break repair, the role of this mutation in genome evolution and maintaining genome instability during the expansion of the primary tumor mass is not well understood. To investigate these questions, we developed a novel method for single-cell, single-molecule (SCSM) sequencing. SCSM uses a Tn5 transposase to directly fragment and ligate adapters for PCR amplification, thereby omitting the whole-genome-amplification (WGA) step, which introduces technical noise into single-cell sequencing datasets. This approach provides single-molecule data by positional barcoding, reducing WGA artifacts that are typically associated with amplification bias. We further utilize a dual-barcoding approach and acoustic liquid transfer technology to increase throughput (N=384) and reduce cost to $1 per cell using nanoliter volumes. We applied SMSC to sequence copy number profiles from ~1000 single cells from two patients with BRCA2-positive breast tumors. In both cases we identified several major clonal subpopulations that shared a set of truncal CNAs, suggesting that they evolved from a single normal epithelial cell in the breast, not multiple initiating cells. We also identified many small subclonal CNAs that further diversified the major clones, which suggests that copy number evolution was ongoing during the expansion of the primary tumor mass. These data demonstrate the technical feasibility of SMSC sequencing, and further show that minor copy number evolution is ongoing in BRCA-positive breast cancer patients.

Citation Format: Haowei Du, Alexander Davis, Ruli Gao, Medina Colic, Emi Sei, Min Hu, Angelica Gutierrez Barrera, Anna Casasent, Constance Albarracin, Banu Arun, Nicholas E. Navin. Single-molecule single-cell DNA sequencing identifies ongoing copy number evolution in BRCA breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2192.
Abstract 2207: High-risk human papillomavirus detection in head and neck cancers using saliva
Authors: Tang Kai D , Perry Chris , Punyadeera Chamindie
Published: August 2018

Human papillomavirus (HPV), a virus vital to the etiology of cervical cancer, is strongly associated with the development of head and neck cancer. Therefore, it is pivotal to develop a noninvasive and cost-effective approach for detecting oral HPV. Accumulating evidence suggested the usefulness of salivary oral rinse as a diagnostic fluid to detect oral HPV DNA within a clinical setting. However, there is little known about the HPV DNA prevalence and type distribution in unstimulated whole mouth saliva (UWMS). In the current study, we show a positive correlation of HPV-16 E2 (r = 0.95, p < 0.0001) and E6/7 (r = 0.93, p < 0.0001) relative copy number as well as high-risk HPV genotypes (HPV 16, 18 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68) and fold change difference between the relative copy numbers of E2 and E6/7 (r = 0.46, p < 0.0098) in both salivary oral rinse and UWMS samples collected from OPC patients. More importantly, in line with the previous study, among HPV-16 positive head and neck cancer cases, most often a mixed HPV-16 form (episomal and integrated) was found in both saliva sampling methods. In conclusion, regardless of the sampling method, detection of HPV in saliva is an attractive, noninvasive method that could change the need for invasive biopsies in head and neck cancer patients.

Citation Format: Kai D Tang, Chris Perry, Chamindie Punyadeera. High-risk human papillomavirus detection in head and neck cancers using saliva [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2207.
Abstract 2220: Autoantibody detection of high-grade serous ovarian cancer with paraneoplastic antigens
Authors: Hurley Laura C. , Levin Nancy K. , Chatterjee Madhumita , Tainsky Michael A.
Published: August 2018

Improved early detection methods for ovarian cancer are necessary as the majority of cases present at late stage metastatic disease with a poor prognosis. Early stages of tumor development initiate an immune response, eliciting antibodies that target tumor associated antigens. Paraneoplastic neurological syndromes are rare autoimmune disorders that develop when the unregulated immune response against a tumor also targets healthy cells, due to shared tumor antigen expression with nervous system and muscle tissue. As these syndromes generally precede detection of a tumor, paraneoplastic antibodies are previously unexplored candidate biomarkers for early diagnosis of ovarian cancer. We have detected paraneoplastic antibodies in serum samples from patients with high-grade serous ovarian cancer (HGSOC) that did not present with paraneoplastic neurological syndrome symptoms using paraneoplastic diagnostic line blots. Ovarian cancer specific epitopes discovered previously in our laboratory by phage-display biopanning were evaluated for both homology to paraneoplastic antigens and for reactivity with paraneoplastic neurological syndrome patient sera. Western blot screening revealed a panel of paraneoplastic antigens that distinguished HGSOC patient sera autoantibody reactivity from healthy and benign sera. An indirect ELISA for measuring patient serum autoantibody reactivity was developed and correlated with western blot results. A panel consisting of 8 antigens: 5 paraneoplastic antigens, 2 well-characterized tumor associated antigens, and a non-reactive control was selected for screening on ELISA against patient serum samples representing each group of HGSOC early stage, HGSOC late stage, healthy, and benign. Biomarkers identified can contribute to an autoantibody diagnostic panel for early clinical diagnosis of ovarian cancer, which would allow for timely therapeutic intervention with potential to improve patient outcome.

Citation Format: Laura C. Hurley, Nancy K. Levin, Madhumita Chatterjee, Michael A. Tainsky. Autoantibody detection of high-grade serous ovarian cancer with paraneoplastic antigens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2220.
Abstract 2229: Mammography assessment of microcalcifications using a pixel detector system
Authors: Bernal Carlos Ávila , Roque Gerardo , Rueda Roberto , Racedo Jorge
Published: August 2018

Breast cancer is a major public health problem being the most frequently diagnosed malignancy and the second leading cause of dead from cancer among women in the United States. In 2015, there were expected around 231,840 new cases of invasive breast cancer, as well as 60,290 cases of in situ breast cancer, and 40,290 deaths. Worldwide, it represents 23% of the total cases diagnosed of cancer and 14% of the cancer deaths in female. Diagnosing breast cancer before it has the potential to invade surrounding tissue and metastasize can increase the chance of survival, reduce poor prognosis and the need of aggressive treatment. This is one of the main goals of early diagnosis that advocates mammography, the clinical examination and the breast self-examination as screening modalities for breast cancer. Recently, other technologies have been proposed like ultrasound and magnetic resonance imaging (MRI). Although these screening methods have reduced the relative risk of death, they have some limitations in some population groups. The aim of this work is adapting and testing a semiconductor pixel detector, Timepix in a custom-swine breast phantom to evaluate its technical feasibility to introduce this technology in a clinical setting for mammography assessment based on microcalcification detection. Swine model is commonly used in medical research based on anatomical and histopathological characteristics closely resemble those of humans, and this is an advantage over the wax-based phantoms that contains aluminum oxide (Al2O3) specks, nylon fibers and other inclusions to mimic microcalcifications and histopathological structures. The Timepix detector was used together with a Tungsten microfocus X-ray to detect hydroxyapatite crystals mimicking malignant microcalcifications with sizes ranged between 153-827μm, embedded into the swine phantom. To compare the detection performance in the swine phantom, a commercial phantom has been used (Model 015 CIRS Inc., Norfolk, VA, US). Both phantoms were tested on a clinical mammography system (Selenia Dimensions AWS 5000 ET19) and by using the experimental setup with the Timepix. This approach has potential to be used for mammography screening in different population groups based on its performance in microcalcifications detection. The results are highly relevant for further studies of the feasibility of pixel detectors for risk assessment and early diagnosis of breast cancer.

Citation Format: Carlos Ávila Bernal, Gerardo Roque, Roberto Rueda, Jorge Racedo. Mammography assessment of microcalcifications using a pixel detector system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2229.
Abstract 2237: Diclofenac as a dual inhibitor of cyclooxygenase and aldo-keto-reductase 1B10 inhibits pancreatitis-enhanced carcinogenesis in LSL-Kras
G12D
-Pdx-1-Cremice
Authors: Liao Jie , Sun Leyu , Li Haonan , Xia Rong , You Xiaoming , Xu Dandan , Yang Guang-Yu
Published: August 2018

Diclofenac is one of non-steroid anti-inflammatory drugs and is recently identified as a competitive inhibitor of aldo-keto reductase family 1B10 (AKR1B10). AKR1B10 is an NADPH-dependent enzyme that exhibits lipid substrate specificity, especially for farnesyl and geranylgeranyl involved in protein prenylation (such as for Kras) and plays an oncogenic role in pancreatic carcinogenesis. In the present study, we determined the chemopreventive effects and mechanism of diclofenac on inhibiting pancreatitis-carcinogenesis in LSL-KrasG12D/Pdx1-Cre mice (called Pankras mice), particularly on Kras prenylation. Pancreatitis was induced by single i.p. injection of Cearulein (250ug/Kg body weight) for 5-week old mice, and one week after caerulein treatment, Pankras mice were fed an AIN-93M diet or a diet with 5 or 20ppm diclofenac (n=12 mice/group) for 7 months. The results showed that Diclofenac significantly reduced the severity of chronic pancreatitis, as measured by the extent of acini loss, inflammatory cell infiltration and stromal fibrosis. The progression of low-grade mPanIN I to high-grade mPanIN II/III and to invasive carcinoma was significantly suppressed and the tumor incidence significantly reduced to 50% and 17% in the mice treated with either 5ppm or 20 diclofenac compared to 86% in Pankras mice. Inhibition of membrane-bound mutant Kras (prenylated) and its transmitted phosphorylation of mitogen-activated protein kinase's kinase/extracellular signal-regulated kinases were demonstrated in pancreatic tissues by western blot assay. Analysis of the eicosanoid profile revealed a significant reduction of prostaglandin E2. These results indicate that diclofenac is a highly potential agent for preventing chronic pancreatitis and carcinogenesis, mainly via targeting mutant Kras and inflammation (Supported by NIH R01 CA164041).

Citation Format: Jie Liao, Leyu Sun, Haonan Li, Rong Xia, Xiaoming You, Dandan Xu, Guang-Yu Yang. Diclofenac as a dual inhibitor of cyclooxygenase and aldo-keto-reductase 1B10 inhibits pancreatitis-enhanced carcinogenesis in LSL-KrasG12D-Pdx-1-Cremice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2237.
Abstract 2243: Cell-phone radiofrequency enhances angiogenesis and stimulates cell invasion of human head and neck cancer cells
Authors: Moustafa Ala-Eddin Al
Published: August 2018

Today, cell-phone is the most widespread technology globally. It has been suggested that cell-phone radiofrequency (RF) use may increase the risk of human brain and probably head cancers. However, the outcome of cell phone RF on head and neck (HN) cancer progression has not been explored yet. Thus, first we examined the outcome of cell-phone RF on angiogenesis using the chorioallantoic membrane (CAM) of the chicken embryo as a model. Then we investigated the effect of cell-phone RF on cell invasion and colony formation in soft agar of two human HN cancer cell lines. Our data revealed that cell-phone RF promotes angiogenesis of the CAM. In addition, cell-phone RF enhances cell invasion and colony formation of human HN cancer cells; this is accompanied by a down-regulation of E-cadherin expression. Regarding the mechanism of cell-phone RF on angiogenesis, cell invasion and colony formation, we found that cell-phone RF activates Erk1 and Erk2 in our experimental models which could be the main pathway behind these events. These data suggest that cell-phone RF enhances HN cancer progression by stimulating angiogenesis, cell invasion and tumor formation via Erk1 and Erk2.

Citation Format: Ala-Eddin Al Moustafa. Cell-phone radiofrequency enhances angiogenesis and stimulates cell invasion of human head and neck cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2243.
Abstract 2274: Cancer genomics visualization and interpretation using UCSC Xena
Authors: Goldman Mary , Craft Brian , Zhu Jingchun , Haussler David
Published: August 2018

The UCSC Xena platform (http://xena.ucsc.edu/) allows biologists and bioinformaticians to securely analyze and visualize functional genomics data. Our unique Visual Spreadsheet shows multiple data types side by side enabling discovery of correlations across and within genes and genomic regions. Dynamic Kaplan-Meier survival analysis assesses survival stratification in addition to scatter plots, bar graphs, and boxplots all shown with statistical tests.

In addition to the commonly available SNPs, INDELs, CNV, and gene expression datasets, we support DNA methylation, exon-, transcript-, miRNA-, lncRNA-expression and structural variants. We also support clinical data such as phenotypes, subtype classifications and biomarkers. Our new whole genome views allow users to easily visualize non-coding regions for both copy number variation and somatic mutations. All of our data is available for download via our python API or through AWS S3 buckets.

Our expanding public Xena Data Hubs currently host 1500+ datasets from more than 35 cancer types, as well as Pan-Cancer datasets. In addition to serving seminal cancer genomic datasets to the scientific community, including the latest from the GDC, TCGA, TARGET, and ICGC, we also host 'normal tissue' datasets from GTEx. A recompute of TCGA, TARGET and GTEx datasets through the same bioinformatics pipeline allows users to compare expression between tumor and normal tissues.

In addition to exploring these public datasets, the UCSC Xena Browser can easily display an investigator's genomic and clinical data on their own Xena Hub. By empowering users to install and load data into their own hub, our architecture ensures that the investigator's data remains private. The lightweight Xena Data Hubs are straightforward to install on Windows, Mac and Linux operating systems and loading data is easy using either our application or command line interface.

Citation Format: Mary Goldman, Brian Craft, Jingchun Zhu, David Haussler. Cancer genomics visualization and interpretation using UCSC Xena [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2274.
Abstract 2280: Systematic analysis of causal noncoding mutations in pediatric B-cell acute lymphoblastic leukemia
Authors: He Bing , Gao Peng , Ding Yang , Chen Chia-Hui , Kim Hannah , Hunger Stephen P. , Tasian Sarah K. , Tan Kai
Published: August 2018

B cell acute lymphoblastic leukemia (B-ALL) is the most prevalent childhood hematological malignancy and the leading cause of childhood cancer-related mortality. To date, the molecular pathogenesis of B-ALL has not been completely defined, limiting our ability to develop targeted therapies. Despite great advances in identifying mutations in cancer patients, the functional consequences of noncoding mutations are still difficult to interpret. Transcriptional enhancers are key determinants of tissue-specific gene expression. Several recent studies have reported novel mutations in cancer genome that disrupt enhance function and thus expression of their target genes. However, systematic detection of noncoding mutations that perturb either enhancer sequence or enhancer-promoter (EP) interaction is still challenging. Such analysis can help to identify novel driver mutations and improve our understanding of the disease.

Here we introduce a novel algorithm for identifying causal mutations that disrupt enhancer function and target gene expression in B-ALL. The algorithm takes as input

whole genome sequencing (WGS) and RNA-Seq data to predict causal noncoding mutations. We apply the algorithm to analyze data from 163 B-ALL patients and identify 332 noncoding mutations that disrupt EP interactions and gene expression. Our analysis recapitulate previously known translocations such as t(14;X) that leads to CRLF2 overexpression, as well as novel causal translocations that leads to deregulation of TMEM106A and MIR663B. Systematic analysis of the identified mutations indicated that SNVs in enhancer region have a higher variant allele frequency (VAF), suggesting enhancer mutations likely occur earlier than coding mutations during oncogenesis. In addition, pathway analysis show that the majority (57%) of mutations perturbing metabolic pathways are noncoding mutations. Further analysis and experimental follow-up of the predicted noncoding mutations may reveal novel insights into the pathogenesis of B-cell ALL.

Citation Format: Bing He, Peng Gao, Yang Ding, Chia-Hui Chen, Hannah Kim, Stephen P. Hunger, Sarah K. Tasian, Kai Tan. Systematic analysis of causal noncoding mutations in pediatric B-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2280.
Abstract 2294: Customizable weighted DNA copy-number networks inform oncogenic pathway alterations and chemoresistance risk
Authors: Delaney Joe Ryan , Stupack Dwayne G.
Published: August 2018

Cancer is driven by mutations of many types: single nucleotide variants, insertion-deletion events within coding exons, and prolific DNA copy-number alterations (CNAs). CNAs have been often viewed as a passenger event due to seemingly inconsistent patterns between tumors and a large fraction of the genome altered, preventing traditional statistical analysis. Here, we present a tool which incorporates phenotypic data including haploinsufficiency and triploproficiency of genes and protein-protein interaction studies, which enables the identification of consistently altered pathways in cancer. This tool, HAPTRIG (for HAPloinsufficient and TRIplosensitive Gene) can be used with RNA, log2 CNA, absolute CNA data, or any other normalized gene-level data. As part of the pathway scoring process, control CNA networks are generated to provide a permuted-genome control, enabling detection of alterations in very heterogeneous cancer backgrounds. The customizable gene-scores which build these networks allow prioritization of altered network hubs: single genes which have exceptional influence within an altered pathway, facilitating hypothesis-testing in cell and animal models. A beta-version was validated in a recent publication from our lab to better predict tumor suppressor genes and oncogenes than Gene Set Enrichment Analysis, and additionally identified targetable pathway hubs which improved murine treatment in ovarian cancer chemo-resistant models. However, its applicability was limited in the beta. Now HAPTRIG can work with any user-supplied human dataset, not just TCGA samples, is an order of magnitude faster, able to run in parallel processors for unlimited speed improvement, and can produce pan-pathway outputs. The tool can use expected background rates from permuted data or compare to a second control dataset, which can be used to compare altered CNA pathways in tumor subtypes or unusual alterations of RNA compared to CNAs, among many other possibilities. We provide this tool for free community use online and in App form, so molecular biologists without bioinformatics training may produce well-informed hypotheses. We find that altered CNA pathways can predict chemoresistance risk groups within tumor types. A tumor suppressor gene hub was found to accelerate tumorigenesis upon deletion in a spontaneous mouse model. Overall, HAPTRIG represents a user-friendly tool to better understand a whole new landscape of tumor mutations: that of copy number alterations.

Citation Format: Joe Ryan Delaney, Dwayne G. Stupack. Customizable weighted DNA copy-number networks inform oncogenic pathway alterations and chemoresistance risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2294.
Abstract 2304: In vivo E2F reporting reveals efficacious schedules of MEK1/2-CDK4/6 targeting and mTOR-S6 resistance mechanisms
Authors: Teh Jessica , Cheng Phil F. , Purwin Timothy J. , Nikbakht Neda , Patel Prem , Chervoneva Inna , Keibler Ines , Kim HooKim , Davies Michael A. , Kwong Lawrence N. , Levesque Mitch P. , Dummer Reinhard , Aplin Andrew E.
Published: August 2018

Targeting cyclin dependent kinases 4 and 6 (CDK4/6) represents a viable therapeutic option in combination with BRAF inhibitor and/or MEK inhibitor in different genetic subsets of melanoma. However, continuous dosing of MEK inhibitor (MEKi) plus CDK4/6 inhibitor (CDK4/6i) elicits toxicities in patients. Utilizing an in vivo E2F reporter system, we analyzed the efficacy of MEKi plus CDK4/6i schedules in a quantitative and temporal manner. Continuous MEKi with intermittent CDK4/6i led to more complete responses as compared to either continuous CDK4/6i with intermittent MEKi or intermittent dosing of both drugs. Nevertheless, some tumors acquired resistance. Phospho-proteomic analysis of resistant tumors revealed increased phosphorylation of ribosomal S6 protein (RPS6). These data were supported by staining of patient biopsies from clinical trials, which also indicated that high phospho S6 levels may serve as a predictor of response to CDK4/6i plus targeted inhibitors. Enhanced phospho S6 provided a therapeutic window for the mTORC1/2 inhibitor, AZD2014, in MEKi plus CDK4/6i-resistant tumors. Mechanistically, aberrant regulation of NRAS was associated with resistance and sufficient to mediate resistance. This study highlights the use of an in vivo reporter model for optimization of schedules and supports targeting the mTORC1/2-S6 pathway as a salvage option to overcome MEKi plus CDK4/6i resistance.

Citation Format: Jessica Teh, Phil F. Cheng, Timothy J. Purwin, Neda Nikbakht, Prem Patel, Inna Chervoneva, Ines Keibler, HooKim Kim, Michael A. Davies, Lawrence N. Kwong, Mitch P. Levesque, Reinhard Dummer, Andrew E. Aplin. In vivo E2F reporting reveals efficacious schedules of MEK1/2-CDK4/6 targeting and mTOR-S6 resistance mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2304.
Abstract 2321: Molecular crosstalk between ferroptosis and apoptosis: Emerging role of ER stress-induced p53-independent PUMA expression
Authors: Lee Young-Sun , Hong Se Hoon , Lee Dae-Hee , Jo Min J. , Jeong Yoo A. , Kwon William T. , Choudry Haroon A. , Bartlett David L. , Lee Yong J.
Published: August 2018

Ferroptosis is a type of programmed cell death that depends on iron and is characterized by the accumulation of lipid peroxides. In the present study, we investigated the nature of the interplay between ferroptosis and other forms of cell death such as apoptosis. Human pancreatic cancer PANC-1 and BxPC-3 and human colorectal cancer HCT116 cells were treated with ferroptotic agents such as erastin and artesunate (ART) in combination with the apoptotic agent tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). We observed synergistic interaction of erastin or ART with TRAIL as determined by cell death assay, caspase activation, poly [ADP-ribose] polymerase 1 (PARP-1) cleavage, flow cytometry analysis, and lipid peroxidation assay. Moreover, erastin and ART induced endoplasmic reticulum (ER) stress and promoted p53 upregulated modulator of apoptosis (PUMA) expression via C/EBP-homologous protein (CHOP). Synergy of erastin/ART and TRAIL was abolished in PUMA-deficient HCT116 cells and CHOP-deficient mouse embryonic fibroblasts, but not in p53-deficient HCT116 cells. The results suggest the involvement of the p53-independent CHOP/PUMA axis in response to ferroptosis inducers, which may play a key role in ferroptotic agent-mediated sensitization to TRAIL-induced apoptosis.

Citation Format: Young-Sun Lee, Se Hoon Hong, Dae-Hee Lee, Min J. Jo, Yoo A. Jeong, William T. Kwon, Haroon A. Choudry, David L. Bartlett, Yong J. Lee. Molecular crosstalk between ferroptosis and apoptosis: Emerging role of ER stress-induced p53-independent PUMA expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2321.
Abstract 2324: Docosahexaenoic acid-induced Nrf2 may be correlated with cell death by amplification of oxidative stress via induction of klf9 in cervical cancer cells
Authors: Jing Kaipeng , Shin Soyeon , Han Seung-Hyeon , Jeon Young-Joo , Heo Jun-Young , Kweon Gi-Ryang , Park Seung-Kiel , Park Jong-Il , Lim Kyu
Published: August 2018

NF-E2-related transcription factor-2 (Nrf2) is a key transcriptional factor regulating antioxidant gene expression and protection from oxidant damage. Docosahexaenoic acid (DHA) as one of ω3-polyunsaturated fatty acids has anticancer action through several mechanisms. Here we report that DHA-induced Nrf2 is related to cell death, not survival in HeLa cell. We confirmed DHA-induced apoptotic cell death using PARP cleavage, Anexin V staing, and TUNEL positive staining assay. DHA-triggering ROS production increased the level Nrf2 and decreased keap1 in dose- and time-dependent manner. Increased Nrf2 by DHA was partially Keap1 dependent. DHA activated Nrf2 signaling by increasing its translation and the Nrf2 was translocated from cytosol to nucleus. Upregulation of DHA-mediated Nrf2 was also confirmed by increase of heme oxygenase-1 (HO-1) expression. DHA-induced Nrf2 increased the level of Kruppel-like factor 9 (klf9) and then decreased thioredoxin reductase 2 (Txnrd2) in dose- and time-dependent manner. These results suggest that DHA-induced ROS increases Nrf2 and the Nrf2 is related to cell death by increase of klf9 and decrease of Txnrd2 in HeLa cells. Thus, utilization of ω3-PUFAs may represent a promising therapeutic approach for chemoprevention and treatment of human cervical cancer [This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST) (NRF-2015R1D1A1A01056887) and by the framework of international cooperation program managed by National Research Foundation of Korea (2015K2A2A6002008)]

Citation Format: Kaipeng Jing, Soyeon Shin, Seung-Hyeon Han, Young-Joo Jeon, Jun-Young Heo, Gi-Ryang Kweon, Seung-Kiel Park, Jong-Il Park, Kyu Lim. Docosahexaenoic acid-induced Nrf2 may be correlated with cell death by amplification of oxidative stress via induction of klf9 in cervical cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2324.