bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 531: MiR-199a-5p is a biomarker for and regulator of epithelial-mesenchymal transition in triple-negative breast cancer patients
Authors: Shin Vivian Y. , Siu Man T. , Ho John C. , Kwong Ava
Published: May 2015

Objectives: Triple-negative breast cancer (TNBC) accounts for 15-20% of all breast cancer, and is characterized by the absence of estrogen receptor, progesterone receptor and human epidermal growth factor receptor. The lack of targeted therapy is a major obstacle for treating against this aggressive subtype, hence the search of specific biomarkers may use as potential diagnostic marker and perhaps a therapeutic target for TNBC. Methods: Plasma samples from patients with TNBC and non-TNBC were recruited for miRNA profiling. By using miRCURY LNA array containing 730 miRNAs, we compared the differential miRNA expressions in plasma of patient with TNBC (n=5) and non-TNBC (n=5), as well as healthy controls (n=5). Selected miRNAs were further validated in an independent cohort (n=250) using real-time RT-PCR. Functional study of miRNA was also carried out in the cell lines. Results: Microarray data revealed miR-16, miR-21 and miR-199a-5p have differentially expression between TNBC and non-TNBC. We found that miR-16, miR-21 and miR-199a-5p were underexpressed in TNBC cases when compared with healthy controls. Moreover, post-operative expression levels of miR-16, miR-21 and miR-199a-5p were significantly increased than that of pre-operative plasma of TNBC. We then stratified the patients by TNM stage and associate with miRNA expression level. Plasma miR-199a-5p expression in TNBC patients had significant difference when compared with healthy controls (stage I, p<0.002; stage II, p<0.001; stage III, p<0.011). Transfection of miR-199a-5p mimic significantly reduced cell proliferation and restored the epithelial-mesenchymal transition (EMT) markers (E-cadherin, ZEB1 and TWIST2). Conclusions: Our data implicate that miR-199a-5p is a potential marker for discriminating TNBC cases and non-TNBC cases. The association of miR-199a-5p with EMT markers uncovers an important pathway in metastatic breast cancer. This study provides insights for the potential use of miRNA as diagnostic marker and targeted therapy for the treatment of TNBC.

Citation Format: Vivian Y. Shin, Man T. Siu, John C. Ho, Ava Kwong. MiR-199a-5p is a biomarker for and regulator of epithelial-mesenchymal transition in triple-negative breast cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 531. doi:10.1158/1538-7445.AM2014-531
Abstract 5312: Quantitative proteomic analysis of cell-surface membrane proteins: Biomarker discovery in esophageal squamous cancer
Authors: Harada Emi , Serada Satoshi , Takahashi Tsuyoshi , Fujimoto Minoru , Naka Tetsuji
Published: May 2015

Background. Esophageal squamous cell cancer (ESCC) is associated with a poor prognosis and high recurrence rate. Identification of proteins that are useful for prognostic assessment and therapeutic targets in ESCC is required. Quantitative proteomic analysis provides a powerful approach in screening for alterations in protein levels. An analysis of the differential expression of cell-surface membrane proteins would be useful for identification of proteins associated with cell proliferation, cell migration, drug resistance and therapeutic target for antibody-based therapy.

Purpose of study. To identify cell-surface membrane proteins overexpressed in ESCC compared with normal esophageal epithelial cells, which may represent novel biomarkers of disease and therapeutic targets.

Procedures. We performed a biotinylation-based approach for cell-surface membrane enrichment combined with iTRAQ (isobaric tags for relative and absolute quantitation) technology using nano-LC-MS/MS analysis, to identify cell surface proteins overexpressed in ESCC cell lines compared with control normal esophageal epithelial cell line.

Results. By combining biotinylation of cell-surface membrane proteins and iTRAQ analysis, 1635 proteins were identified, which contained 402 cell surface membrane proteins. We identified overexpression of 12 membrane proteins, whose expression increased more than twofold in at least four of six ESCC cell lines compared with a normal esophageal epithelial cell line (HEEpic). By this proteomic approach, we identified several tumor antigens which included antigens previously associated with ESCC and antigens not previously reported in this disease. Furthermore, we also successfully identified novel antigen associated with proliferation of ESCC. Cell surface expression of this antigen on ESCC was confirmed by FACS analysis and immunohistochemistry. By transfection of siRNA specific for this novel antigen, significant growth suppression was shown by WST8 assay and induction of apoptosis was detected by caspase-3 assay.

Conclusions. By using a high throughput cell-surface membrane proteomic analysis combining biotinylation of cell-surface membrane protein and iTRAQ technology, several ESCC candidate antigens were identified. Further studies on the physiological role of novel tumor antigens overexpressed in ESCC and their application as biomarkers/therapeutic targets are underway.

.

Note: This abstract was not presented at the meeting.

Citation Format: Emi Harada, Satoshi Serada, Tsuyoshi Takahashi, Minoru Fujimoto, Tetsuji Naka. Quantitative proteomic analysis of cell-surface membrane proteins: Biomarker discovery in esophageal squamous cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5312. doi:10.1158/1538-7445.AM2014-5312
Abstract 5318: LC-MS/MS quantification of proteins CD47 and SIRPA in cell subtypes selected by flow cytometry from blood
Authors: Fernandez-Metzler Carmen , Capocasale Renold
Published: May 2015

Flow cytometry and mass spectrometry are widely used analytical tools in cancer research. Flow cytometry is known for cell counting, cell sorting and cancer biomarker discovery. Mass spectrometry is unparalleled in its ability to selectively detect and quantify target analytes at the molecular level. The combination of flow cytometry to isolate specific cell subtypes from biological fluids such as blood and mass spectrometry to quantify proteins contained in the selected cells provides a new approach to studying protein expression in specific cell subtypes. We have used this combination to investigate the normal levels of CD47 and SIRPA proteins in CB8+ T-cells, CD4+ T-cells, CD14+ monocytes, CD33+ myeloid cells and CD56+ NK cells isolated from blood specimens as a first step toward better understanding of how the CD47/SIRPA protein levels in these cells are affected by cancer and cancer treatment.

Citation Format: Carmen Fernandez-Metzler, Renold Capocasale. LC-MS/MS quantification of proteins CD47 and SIRPA in cell subtypes selected by flow cytometry from blood. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5318. doi:10.1158/1538-7445.AM2014-5318
Abstract 5320: Novel computational methods reveal subtle clonal mosaicism
Authors: Scheet Paul , Xia Rui , Lucas F. Anthony San , Hahn Christina , Fowler Jerry , Vattathil Selina
Published: May 2015

Recent genome-wide surveys have revealed age-related genetic mosaicism and established a link between clonal mosaicism and risk of hematological and solid-tumor cancers (Laurie et al, 2012, Nat Genet, 44:642; Jacobs et al, 2012, Nat Genet, 44:651; Forsberg et al, 2012, AJHG, 90:217). Existing methods to identify chromosomal aberrations leading to mosaic allelic imbalance (AI) rely on the detection of increased variance of the estimated within-sample allele frequencies at heterozygous loci, ignoring the dependence among allele frequencies in regions of an AI-inducing event, such as a deletion or copy-neutral loss of heterozygosity (LOH), expected from the loss or gain of a chunk of an inherited chromosome. As a result, they break down when the proportion of DNA from an aberrant source is below 10-15%. Here we present a suite of new methods (hapLOH, J-LOH, hapLOHseq) that harness the important information contained in the germline haplotypes to help distinguish signal from noise, accommodate multiple samples of different tumor purities (to deconvolute aberration type and tumor purity) and infer co-occurrence of aberrations in heterogeneous mixtures. For example, our initial method, hapLOH (Vattathil & Scheet, 2013, Gen Res 23:152), can identify 10 Mb regions with just 4% of the signal coming from the tumor genome in data simulated from a series of experiments from a 317K SNP microarray. Application of hapLOH to data analyzed by Laurie et al (2012) indicates that we have substantially greater sensitivity to detect clonal mosaicism, particularly events harbored in a small proportion of cells (< 5-10%). We identify more than twice as many mosaic events, demonstrating the potential role for our methods to aid in profiling cancer risk. Our suite of tools is designed for both microarray and next-generation sequencing data and is available at scheet.org.

Citation Format: Paul Scheet, Rui Xia, F. Anthony San Lucas, Christina Hahn, Jerry Fowler, Selina Vattathil. Novel computational methods reveal subtle clonal mosaicism. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5320. doi:10.1158/1538-7445.AM2014-5320
Abstract 5327: Using CellMiner for gene expression, DNA copy number, microRNA transcript levels, variant status, drug activity, and their integration for systems pharmacology for the NCI-60
Authors: Reinhold William C. , Sunshine Margot , Varma Sudir , Morris Joel , Kohn Kurt , Doroshow James , Pommier Yves
Published: May 2015

Molecular biology and pharmacology are being transformed by high-throughput data. Access, and integration of this data, however, remains difficult. The NCI-60 cancerous cell lines are arguably the premier model for data integration and systems pharmacology. To make this data accessible for both bioinformaticists and non-bioinformaticists, we have developed the CellMiner set of web-based tools (http://discover.nci.nih.gov/cellminer). These tools currently or in the near future will provide “Cell line signatures” for gene and microRNA transcript expression, DNA copy number variation, genetic variation, and drug or compound activity. This data includes relative levels of transcript expression for 26,065 genes, 360 microRNAs, activities of 19,940 compounds including 110 Food and Drug Administration (FDA)-approved and 53 in clinical trial drugs, and percent conversions of 16,381 genetic variants (both germline and somatic). Current or upcoming tools facilitating the combination of this data include i) “Pattern comparison”, which provides correlations to a users input pattern to transcript and microRNA expression and compound/drug activity, ii) “Cross correlation”, which provides all correlations between up to 150 input genes, microRNAs, and compounds or drugs, iii) “Genetic variation versus drug visualization”, which provides a rapid visualization of potential drug: gene DNA variant relationships, and iv) “Genetic variant summation”, which provides a synopsis of mutational burden on any pathway of interest for up to 150 genes. These tools allow the user to flexibly query the data for potential relationships between molecular and pharmacological parameters, in a manner specific to that users area of expertise and interest.

Citation Format: William C. Reinhold, Margot Sunshine, Sudir Varma, Joel Morris, Kurt Kohn, James Doroshow, Yves Pommier. Using CellMiner for gene expression, DNA copy number, microRNA transcript levels, variant status, drug activity, and their integration for systems pharmacology for the NCI-60. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5327. doi:10.1158/1538-7445.AM2014-5327
Abstract 533: MicroRNA486-5p is a KRas target involved in promoting cell proliferation in lung cancer
Authors: Aoki Mateus N. , Salviatto Amanda C. P. , Lobo Tatiana C. C. , Carreira Ana Cláudia O. , Sogayar Mari C. , Basseres Daniela S.
Published: May 2015

KRAS-induced lung cancer is a very common disease, for which there are currently no effective therapies. Direct targeting of KRAS has failed in clinical trials and intense efforts are underway to identify KRAS targets that play a crucial role in oncogenesis. One promising KRAS-regulated pathway that has so far been overlooked is the microRNA pathway. Even though many microRNAs that regulate expression of KRAS are known, microRNAs regulated by oncogenic KRAS remain largely unknown. Our goal was to identify microRNAs regulated by oncogenic KRAS in lung cells that could contribute to the oncogenic phenotype. Due to a reported positive correlation between microRNA486-5p (miR-486-5p) expression and the presence of KRAS mutations in colon cancer specimens, we decided to investigate in lung cells whether KRAS regulates miR-486-5p. For that purpose we used an immortalized human primary lung epithelial cell line (SALEB) and its isogenic KRAS-transformed counterpart (SAKRAS), as well as lung cancer cell lines with either gain-of-function or loss-of-function of KRAS. We found, in all models tested, a positive correlation between expression of oncogenic KRAS and expression of miR-486-5p. We also found a negative correlation between expression of oncogenic KRAS and expression of miR-486-5p targets, including FoxO1, a tumor suppressor. In order to evaluate how miR-486-5p affects Ras-induced oncogenic properties, we transfected miR-486-5p inhibitor oligonucleotides into KRAS-positive lung cancer cell lines H358 and A549. Inhibition of miR-486-5p expression leads to reduced growth in clonogenic assays and reduced MTT viability. This reduction is not associated with increased cell death, but, as measured by 3H-Thymidine incorporation, it is associated with decreased cell proliferation. Interestingly, transfection of miR-486-5p double-stranded RNA mimic oligonucleotides into KRAS negative lung cancer cell line H1703 or into H358 cells with loss of function of KRAS by RNA interference leads to enhanced proliferation and clonogenicity. Taken together, these results indicate, not only that miR-486-5p is a KRAS target in lung cancer, but also that miR-486-5p acts as an oncomiR contributing to KRAS-induced cell proliferation. Further understanding of miR-486-5p targets could uncover novel pathways for KRAS-induced lung cancer therapy design.

Citation Format: Mateus N. Aoki, Amanda C. P. Salviatto, Tatiana C. C. Lobo, Ana Cláudia O. Carreira, Mari C. Sogayar, Daniela S. Basseres. MicroRNA486-5p is a KRas target involved in promoting cell proliferation in lung cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 533. doi:10.1158/1538-7445.AM2014-533
Abstract 5331: GenomeSpace: An environment for frictionless bioinformatics
Authors: Reich Michael M. , Liefeld John , Ocana Marco , Jang Donkeung , Robinson James , Carr Peter , Hill Barbara , Tabor Thorin , Thorvaldsdottir Helga , Regev Aviv , Mesirov Jill P.
Published: May 2015

Over the past several years, cancer genome characterization initiatives such as The Cancer Genome Atlas and the International Cancer Genome Consortium have produced an explosion of genomic data. These efforts, together with the proliferation of repositories for small-molecule screens and large-scale data production efforts to discover the breadth of genomic variation in humans, offer a new era of potential for the understanding of the basic mechanisms of cancer and identification of novel treatments.

Comprehensive analysis of these datasets requires the coordinated use of Web-based applications and data repositories, desktop analysis tools and visualizers, and single-purpose algorithms. However, the effort required to transfer data between tools, convert between data formats, and manage results often prevents researchers from utilizing the wealth of methods available to them. Many integrative genomics and translational “bench to bedside” discoveries are possible with combinations of existing tools, but the necessary transitions between them puts them out of the reach of most researchers.

GenomeSpace, http://www.genomespace.org, is an environment that brings together diverse computational tools, enabling scientists without programming skills to easily combine their capabilities. It aims to offer a common space to create, manipulate and share an ever-growing range of genomic analysis tools. GenomeSpace features support for cloud-based data storage and analysis, multi-tool analytic workflows, automatic conversion of data formats, and ease of connecting new tools to the environment. A set of six “GenomeSpace-enabled” seed tools developed by collaborating organizations provides a comprehensive platform for the analysis of cancer data: Cytoscape (UCSD), Galaxy (Penn State University), GenePattern (Broad Institute), Genomica (Weitzmann Institute), Integrative Genomics Viewer (Broad Institute), and the UCSC Genome Browser (UCSC). Its open architecture has driven its adoption by a number of additional tools, including ArrayExpress, Cistrome, the Cancer Cell Line Encyclopedia, Project Achilles Portal, and Multiple Myeloma Genomics Portal, with new tools and resources being released regularly.

We show how researchers can use GenomeSpace to effortlessly combine the capabilities of all of these tools in several cancer research scenarios.

Citation Format: Michael M. Reich, John Liefeld, Marco Ocana, Donkeung Jang, James Robinson, Peter Carr, Barbara Hill, Thorin Tabor, Helga Thorvaldsdottir, Aviv Regev, Jill P. Mesirov. GenomeSpace: An environment for frictionless bioinformatics. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5331. doi:10.1158/1538-7445.AM2014-5331
Abstract 5332: Comparison of variant calling from whole exome and transcriptome sequencing using CLC Cancer Research Workbench
Authors: Arens Anne , Hein Anne-Mette K. , Appelt Uwe , Joecker Anika , Mønsted Søren , Knudsen Bjarne , Thomson Naomi , Lussier Richard , Boysen Cecilie , Forsberg Roald
Published: May 2015

The now commonplace application of whole exome and genome sequencing in cancer research and diagnostics has allowed for rapid identification of SNPs and InDels in protein coding regions, but neither method is able to reveal situations of incomplete penetrance. That is, while possible cancer causing allele variants can be detected with these methods, this does not mean these alleles are actually expressed. Reasons for this are various and include epigenetic effects and changes, transcription regulation mechanisms, mRNA degradation and epistasis. By contrast, transcriptome sequencing (RNA-seq) can be used to identify the alleles being expressed. This method has the additional benefits of providing insight into the transcript expression levels, expressed allele isoforms and offers the possibility of identifying instances of fusion transcripts. Such knowledge about variants expressed in tumor cells is crucial for the identification of effective drug targets.

Here, we illustrate the benefits of combining whole exome sequencing with RNA-seq by analyzing whole exome and RNA-seq datasets from uveal melanoma samples with our newly developed CLC Cancer Research Workbench. This software suite enables the complete analysis of both approaches, including variant calling, followed by the comparison of the called variants. The analysis will be carried out using user-friendly, automated workflows distributed with the CLC Cancer Research Workbench. In this work, we discuss and compare variants identified in the exome and RNA-seq datasets using our algorithms, and focus particularly on variants identified in the exome data that appear not to be expressed in the tumor samples.

Citation Format: Anne Arens, Anne-Mette K. Hein, Uwe Appelt, Anika Joecker, Søren Mønsted, Bjarne Knudsen, Naomi Thomson, Richard Lussier, Cecilie Boysen, Roald Forsberg. Comparison of variant calling from whole exome and transcriptome sequencing using CLC Cancer Research Workbench. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5332. doi:10.1158/1538-7445.AM2014-5332
Abstract 5339: Deterministic in silico modeling predicts sensitivity of glioblastoma to targeted therapy
Authors: Pingle Sandeep C. , Pastorino Sandra , Muktharavam Rajesh , Jiang Pengfei , Chao Ying , Abbasi Taher , Vali Shireen , Kesari Santosh
Published: May 2015

Glioblastoma (GBM) is an aggressive disease associated with poor survival. The key to developing better diagnostic and therapeutic strategies is accounting for the complexity of GBM biology. This challenge of integrating vast genomic and proteomic data can be addressed by a comprehensive systems modeling approach. To this end, we employ an in silico modeling approach, wherein we utilize genomic and proteomic data to simulate tumor cells and predict drug responses. Using our in silico model, we replicated findings from a recent hypothesis-independent, empirical study that analyzed the sensitivity of hundreds of profiled cancer cell lines to 130 different anticancer agents. Among the drug-mutation associations reported in this study, our in silico model validated ∼85% of the associations. We also used the tumor model to predict sensitivity of patient-derived GBM lines to different targeted therapeutic agents. These analyses showed ∼75% agreement of in silico drug sensitivity with in vitro experimental findings. We aim to use this model to stratify patients for clinical trials. By accurately predicting responses of patient cancer cells to targeted agents a priori, the in silico tumor model provides an innovative approach to personalizing therapy for GBM and promises to improve clinical management of cancers.

Citation Format: Sandeep C. Pingle, Sandra Pastorino, Rajesh Muktharavam, Pengfei Jiang, Ying Chao, Taher Abbasi, Shireen Vali, Santosh Kesari. Deterministic in silico modeling predicts sensitivity of glioblastoma to targeted therapy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5339. doi:10.1158/1538-7445.AM2014-5339
Abstract 5343: Continuing expression of SHP2E76K is required to maintain lung tumors induced by the active SHP2E76K mutant in transgenic mice
Authors: Schneeberger Valentina E. , Luetteke Noreen , Ren Yuan , Foroutan Parastou , Martinez Gary V. , Haura Eric B. , Coppola Domenico , Wu Jie
Published: May 2015

The SHP2 protein tyrosine phosphatase is activated by growth factor receptor oncogenes or by gain-of-function (GOF) missense mutations such as SHP2E76K in human cancer. To study the oncogenic function of GOF SHP2 mutants and the dependency of SHP2 mutant-induced tumors, we established transgenic mice containing the tetO-SHP2E76K transgene. tetO-SHP2E76K mice were bred to CCSP-rtTA mice to direct expression of the transgene in type II pneumocytes to assess the role of the SHP2 mutant in lung adenocarcinoma. When the CCSP-rtTA/tetO-SHP2E76K bitransgenic mice were induced with doxycycline (dox), they developed papillary adenomas that progressed to adenocarcinoma in 6-9 months. This result demonstrates the oncogenic activity of the GOF SHP2 mutant in our mouse model of lung adenocarcinoma. Consistent with previous studies in cultured cells, lung tissues from dox-induced CCSP-rtTA/tetO-SHP2E76K have elevated pGab1, pErk, pSrc and c-Myc. Using magnetic resonance imaging (MRI), we were able to detect lung tumors in the dox-induced CCSP-rtTA/tetO-SHP2E76K bitransgenic mice. To determine if the SHP2E76K-induced lung tumors require continuing expression of the SHP2 mutant for tumor maintenance, dox was withdrawn from the CCSP-rtTA/tetO-SHP2E76K mice after detection of lung tumors by MRI. When these mice were examined again by MRI one month after dox withdrawal, the lung tumors were no longer detectable. Histological evaluation of lung tissues revealed residual hyperplastic lesions as well as evidence of necrosis, while biochemical analysis showed that pGab1, pErk, pSrc and Myc returned to basal levels. Thus, discontinuation of SHP2E76K expression resulted in tumor regression. These data indicate that continuing expression of SHP2E76K is required for maintenance of the SHP2 mutant-induced lung tumors.

Citation Format: Valentina E. Schneeberger, Noreen Luetteke, Yuan Ren, Parastou Foroutan, Gary V. Martinez, Eric B. Haura, Domenico Coppola, Jie Wu. Continuing expression of SHP2E76K is required to maintain lung tumors induced by the active SHP2E76K mutant in transgenic mice. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5343. doi:10.1158/1538-7445.AM2014-5343
Abstract 5378: Actions of nanoparticulate tetraiodothyroacetic acid (Nanotetrac) on human prostate carcinoma xenograft growth, vascularity and integrin response to radiation
Authors: Mousa Shaker A. , Thangirala Sudha , Yalcin Murat , Leith John T. , Hercbergs Aleck , Lin Hung-Yun , Tang Heng-Yuan , Luidens Mary K. , Davis Paul J.
Published: May 2015

Tetraiodothyroacetic acid (tetrac) covalently bound to a nanoparticle (poly[lactic-co-glycolic acid]) (= Nanotetrac) has anti-cancer and anti-angiogenic properties that are initiated exclusively at a cell surface receptor on integrin αvβ3 of cancer cells and dividing blood vessel cells. The anti-cancer activities are pro-apoptotic by multiple mechanisms, disorder gene expression in multiple cancer cell survival pathways and are radiosensitizing. The anti-angiogenic effects involve disruption of actions of VEGF, bFGF, PDGF and EGF. In the present studies, susceptibility of human prostate cancer cell xenografts to activity of Nanotetrac was determined in grafts in the nude mouse or to the chick chorioallentoic membrane (CAM) model and radiosensitivity was estimated in the CAM system. Androgen-sensitive LNCaP cell xenografts in the CAM exposed to Nanotetrac (1 μg/CAM) showed 40% decreases in tumor weight and vascular branch points and 50% reduction in hemoglobin content at 7 d (P < 0.01). LNCaP xenograft volumes in the male mouse were reduced by 50% at 5 days (P < 0.01), approximating the volume of the tumor cell implant. In vivo imaging system (IVIS) scans of orthotopic androgen-independent PC3 cell xenografts in the nude mouse showed substantial reduction in tumor size vs. control (PBS) at 7 d (50% reduction) and at 17 d (75% reduction) post-implantation. Radiation studies in PC3 cell tumors established in the CAM system demonstrated that within 1 h of exposure to 1-2 Gy radiation, there was apparently defensive activation (assumption of ‘open conformation’) of αvβ3. Receptor activation response to radiation was blocked by Nanotetrac. We have shown in other cancer cell lines that Nanotetrac inhibits repair of radiation-induced double-stranded DNA breaks and propose that, based on the current observations, this DNA repair effect is due to inhibition of radiation-caused activation of αvβ3. In summary, examined in two models and acting at the cell surface, Nanotetrac substantially reduces volume/weight and vascularity of human prostate cancer xenografts. The agent also inhibited activation of integrin αvβ3 that is induced by radiation exposure and is seen to be a component of the radioresistance response.

Citation Format: Shaker A. Mousa, Sudha Thangirala, Murat Yalcin, John T. Leith, Aleck Hercbergs, Hung-Yun Lin, Heng-Yuan Tang, Mary K. Luidens, Paul J. Davis. Actions of nanoparticulate tetraiodothyroacetic acid (Nanotetrac) on human prostate carcinoma xenograft growth, vascularity and integrin response to radiation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5378. doi:10.1158/1538-7445.AM2014-5378
Abstract 538: microRNAs as modifiers of stem cell properties in breast cancer: a whole genome approach
Authors: Bonetti Paola , Marzi Matteo J. , nicassio francesco
Published: May 2015

Cancer stem cells (CSCs) are cells with aberrantly regulated stem-like characteristics, such as self-renewal and quiescence. In breast cancer, CSCs have been shown to drive the tumorigenic process and to contribute to the emergence of therapeutic resistance and disease relapse. Based on this background, we decided to focus on the mechanisms that sustain CSC growth, namely self-renewal, to reveal molecules and pathways that control SC biology under physiological and pathological conditions.

Recent research suggests a key role for non-coding RNAs (microRNAs - miRNAs; and long non coding RNAs - lncRNAs) in the control of genetic program that specifies stem cell identity and properties. Nevertheless, we still do not know which non-coding RNAs are involved and how they influence self-renewal or differentiation properties of the normal as well the cancer SC pool in the breast tissue. Based on these premises we aimed at isolating those non-coding RNAs (either lncRNAs or miRNAs) that significantly associates with the self-renewal properties and the content of stem cells in the normal mammary gland and in human breast cancer to search for: i) “markers” that improve the stratification and prognosis of human breast cancer; and ii) “modifiers” (enhancing or suppressing) of self-renewal properties of breast normal and cancer stem cells.

In the long-term, our findings could serve as a basis to develop alternative strategies for the treatment of breast cancer that could radically improve the clinical management of breast cancer.

Note: This abstract was not presented at the meeting.

Citation Format: Paola Bonetti, Matteo J. Marzi, francesco nicassio. microRNAs as modifiers of stem cell properties in breast cancer: a whole genome approach. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 538. doi:10.1158/1538-7445.AM2014-538
Abstract 5389: Discovery of small molecule inhibitors of the interaction between PPARγ and SMRT
Authors: Min Jaeki , Attia Ramy Naguib , Arnold Leggy A , Teske Kelly , Connelly Michele , Lemieux George , Ashrafi Kaveh , Shelat Anang , Guy R. Kiplin
Published: May 2015

The gamma isoform of the peroxisome proliferator-activated receptor (PPARγ) is a ligand-activated nuclear hormone receptor that plays central roles in regulating adipogenesis and maintaining lipid and glucose homeostasis. PPARγ is the molecular target for the thiazolidinedione (TZD) class of antidiabetic drugs. While clinically efficacious, the TZDs exhibit significant side effects that are mechanistically linked to PPARγ including weight gain, edema, and heart failure. SMRT (silencing mediator of retinoid acid and thyroid hormone receptor) and NCoR (nuclear receptor corepressor) are transcriptional corepressors that are critical for normal PPARγ function and act by repressing PPARγ-mediated transcriptional activity in the absence of agonist ligands. In order to explore an alternate method of activating PPARγ signaling, we designed a biochemical assay for the purpose of high-throughput screening (HTS) to identify inhibitors of the interaction between PPARγ and corepressors from our in-house library compounds (292K), which might act as pharmacological agonists. Herein, we report the use of this method to discover small molecule inhibitors of the corepressor interaction with PPARγ. Following hit validation and evaluation, we identified small molecule inhibitors acting through this novel mechanism that potently induce a cellular response similar to the known PPARγ agonist rosiglitazone. In addition, we also confirmed that our hit compound revealed induced adipogenesis in 3T3-L1 cell and reduced fat storage in C.elegans model. These findings highlight the potential of targeting the interaction of PPARγ and SMRT for the discovery of small molecule agonists of PPARγ.

Citation Format: Jaeki Min, Ramy Naguib Attia, Leggy A Arnold, Kelly Teske, Michele Connelly, George Lemieux, Kaveh Ashrafi, Anang Shelat, R. Kiplin Guy. Discovery of small molecule inhibitors of the interaction between PPARγ and SMRT. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5389. doi:10.1158/1538-7445.AM2014-5389
Abstract 5394: A high-throughput screening platform for the identification of small molecule inhibitors of MAP2K4
Authors: Krishna Sankar Narayan , Luan Chi-Hao , Clutter Matthew R. , Mishra Rama K. , Scheidt Karl A. , Anderson Wayne F. , Bergan Raymond C.
Published: May 2015

Prostate cancer (PCa) is the second highest cause of cancer death in United States males. If the metastatic movement of PCa cells could be inhibited, then mortality from PCa could be greatly reduced. Mitogen-activated protein kinase kinase 4 (MAP2K4) has previously been shown to activate pro-invasion signaling pathways in human PCa. Recognizing that MAP2K4 represents a novel and validated therapeutic target, we sought to develop and characterize an efficient process for the identification of small molecules that target MAP2K4. Using a fluorescence-based thermal shift assay (FTS) assay, we first evaluated an 80 compound library of known kinase inhibitors, thereby identifying 8 hits that thermally stabilized MAP2K4 in a concentration dependent manner. We then developed two in vitro MAP2K4 kinase assays to evaluate kinase inhibitory function, one a western-blot based assay employing the biologically relevant downstream substrates, JNK1 and p38 MAPK, and the other an Alphascreen based activity assay. In this manner, we validated the performance of our initial FTS screen. Finally, by coupling our structure-activity relationship data to MAP2K4's crystal structure, we constructed a model for inhibitor binding. It predicted binding of our identified inhibitors to MAP2K4's ATP pocket. We next applied this approach in a high-throughput fashion to over 2200 chemically diverse compounds and identified new inhibitors of MAP2K4. Herein we report the creation of a robust inhibitor-screening platform with the ability to inform the discovery and design of new and potent MAP2K4 inhibitors.

Citation Format: Sankar Narayan Krishna, Chi-Hao Luan, Matthew R. Clutter, Rama K. Mishra, Karl A. Scheidt, Wayne F. Anderson, Raymond C. Bergan. A high-throughput screening platform for the identification of small molecule inhibitors of MAP2K4. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5394. doi:10.1158/1538-7445.AM2014-5394
Abstract 5398: Nanoparticles for image guided focused ultrasound drug delivery
Authors: Thanou Maya , Wright Michael , Centelles Miguel
Published: May 2015

Thermally triggered, PEGylated drug- liposomes are currently in clinical trials. Conventional thermosensitive liposomes (TSLs) lack the labels that would allow tumor imaging upon intravenous injection and a better mark for tissue specific applied hyperthermia (image guidance). We suggest dual- labelled thermosensitive liposomes for focused ultrasound (FUS) induced hyperthermia, triggered-release and functional delivery of the therapeutic anti-cancer drugs to xenograft tumors in response to thermal stimuli in vivo. In addition to labeling for MR Imaging we introduce the use of near infrared (NIR) fluorophores that allow for real time imaging of nanoparticle behavior in the absence of any significant intrinsic tissue background fluorescence, with good to excellent transmission and reduced scattering throughout tissues. We have synthesized these labels as lipid-probe conjugates and using these labels and thermosensitive lipids we have prepared TSL nanoparticles. N`-XenoLight750-N,N-distearylamidomethylamine (XLA750.DSA) and Gadolinium(III) 2-{4,7-Bis-carboxymethyl-10-[(N,N-distearylamidomethyl-N′-amidomethyl]-1,4,7,10-tetraazacyclododec-1-yl}acetic Acid (Gd.DOTA.DSA) were synthesized and characterized. Both lipids were used to prepare TSL nanoparticles carrying the anticancer drugs at substantial encapsulation efficiency. Nanoparticles were tested for their biophysical characteristics (thermal drug release, stability in plasma, size) in vitro. MRI contrast enhancement ability and Near-IR signal were tested in vitro and in vivo. Nanoparticles carrying drugs were injected intravenously in mice bearing tumors. Nanoparticle kinetics in tumors were assessed with optical imaging and at defined time intervals (post injection), FUS (TIPS Phillips: 1.4MHz) was applied for 3-5 min to induce a small increase in temperature from 37°C to 41°C. Optical imaging revealed both substantial nanoparticle accumulation and drug release immediately after and only in tumors treated with focused ultrasound induced (focal) hyperthermia. Tumors treated with both nanoparticles and FUS post injection showed substantial growth inhibition compared to tumors treated with nanoparticles only. The applications of these multifunctional nanoparticles with short and mild hyperthermia could have a transformative effect on cancer chemotherapy.

Citation Format: Maya Thanou, Michael Wright, Miguel Centelles. Nanoparticles for image guided focused ultrasound drug delivery. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5398. doi:10.1158/1538-7445.AM2014-5398
Abstract 5401: Investigation of sub-tumor accumulation of PRINT nanoparticles reveals dose and route of administration dependence on particle association
Authors: Roode Luke , Bo Tao , Perry Jillian , Luft J. Chris , Bear James E. , Davis Ian J. , DeSimone Joseph M.
Published: May 2015

The assessment of nanoparticle accumulation in tumors and other organs uses a whole organ-based approach. These techniques, however, neglect the complex composition of tumors which multiple types of cells other than cancer cells(e.g. endothelial cells, macrophages). For delivery of certain therapeutics, identification of precisely which cells are associating with particles is critical. Using an orthotopic model of melanoma and fluorescently labeled 80x320nm PRINT nanoparticles, we assessed nanoparticle distribution in a cell-type specific manner by flow cytometry. We found that although cancer cells make up 90% of the tumor cells, only a small fraction (1-7%) associate the nanoparticles following intravenous dosing. The fractional association was dependent on the dose used and a plateau is seemingly reached, suggesting a limited number of cells are able to associate with 80x320nm particles. In addition, particle-positive tumor-associated macrophages associated with 4-fold more particles than cancer cells despite constituting approximately 1% of all cells in the tumor. When particles were administered intratumorally, cancer cell association doubles as compared to intravenous dosing. Fluoresence intensity suggests that when dosed intratumorally cancer cells associated with a greater amount of particles, similar to macrophages. Together, these data suggest a biological limitation on the ability of intravenous administration of nanoparticles for nucleic acid delivery and reveal the potential for therapeutic targeting of macrophages.

Citation Format: Luke Roode, Tao Bo, Jillian Perry, J. Chris Luft, James E. Bear, Ian J. Davis, Joseph M. DeSimone. Investigation of sub-tumor accumulation of PRINT nanoparticles reveals dose and route of administration dependence on particle association. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5401. doi:10.1158/1538-7445.AM2014-5401
Abstract 5403: Metronomic docetaxel in PRINT nanoparticles and EZH2 silencing have synergistic antitumor effect in ovarian cancer
Authors: Gharpure Kshipra M. , Chu Kevin S. , Bowerman Charles , Miyake Takahito , Pradeep Sunila , Mangala Lingegowda S. , Han Hee-Dong , Rupaimoole Rajesha , Wu Sherry Y. , Dalton Heather J. , Napier Mary E. , Lopez-Berestein Gabriel , DeSimone Joseph M. , Sood Anil K.
Published: May 2015

Purpose: The purpose of this study was to investigate the combined antitumor effects of metronomic docetaxel-containing PLGA-PRINT nanoparticles and antiangiogenic mEZH2 siRNA incorporated into chitosan nanoparticles (CH-mEZH2 siRNA). Method: In vivo dose-finding studies and therapeutic experiments with PLGA-PRINT-docetaxel and CH-mEZH2 siRNA were conducted in well-established orthotopic mouse models of ovarian cancer (HeyA8 and SKOV3ip1). Antitumor effects were quantified through mean tumor weight and tumor nodule counts. Tumor tissues from these studies were stained to evaluate the proliferation index (Ki67), apoptosis index (cleaved caspase-3), and microvessel density (CD31). Result: Dose-finding studies for PLGA-PRINT-docetaxel revealed all doses (0.5, 1.5, 2 mg/kg for metronomic and 20mg/kg for MTD) significantly reduced tumor burden (p<0.05 for MTD; p<0.01 for metronomic doses). The lowest dose (0.5 mg/kg) reduced tumor weight by ∼80% and was selected for subsequent therapeutic studies. We then tested whether combining PLGA-PRINT-docetaxel particles with CH-mEZH2 siRNA would enhance antitumor effect. CH-mEZH2 siRNA alone reduced tumor weight by ∼70% in both models (p<0.01 for HeyA8; p<0.05 for SKOV3ip1). PLGA-PRINT-docetaxel treatment reduced tumor weight by ∼80% (p<0.01). Combination therapy showed the greatest therapeutic benefit with ∼95% reduction in tumor weight in both models (p<0.001 in HeyA8; p<0.01 in SKOV3ip1). In both the models, the combination therapy resulted in the greatest reduction of tumor nodules. Individual as well as combination therapies showed a significant reduction in proliferation (p<0.001). Metronomic PLGA-PRINT-docetaxel and CH-mEZH2 siRNA monotherapy increased the apoptotic index significantly (p<0.05), whereas the combination therapy had an additive effect (p<0.001). CH-mEZH2 siRNA as well as metronomic PLGA-PRINT-docetaxel therapy resulted in significant reduction in MVD (p<0.01). Conclusion: Metronomic delivery of PLGA-PRINT-docetaxel combined with CH-mEZH2 siRNA is an attractive therapeutic strategy.

Citation Format: Kshipra M. Gharpure, Kevin S. Chu, Charles Bowerman, Takahito Miyake, Sunila Pradeep, Lingegowda S. Mangala, Hee-Dong Han, Rajesha Rupaimoole, Sherry Y. Wu, Heather J. Dalton, Mary E. Napier, Gabriel Lopez-Berestein, Joseph M. DeSimone, Anil K. Sood. Metronomic docetaxel in PRINT nanoparticles and EZH2 silencing have synergistic antitumor effect in ovarian cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5403. doi:10.1158/1538-7445.AM2014-5403
Abstract 5415: Targeted nanoparticle based therapy for the treatment of glioblastoma multiforme: Unprecedented anti-cancer activity in highly drug resistant/refractory mouse models of glioblastoma with novel apoptotic nanoparticles which hone to a cell-surface protein f
Authors: Hudson Sarah , Agemy Lilach , Kotamraju Venkata Ramana , Sharma Shweta , Ruoslahti Erkki , Brunel Florence , MacLaren Ann , Muraski John , Slee Deborah
Published: May 2015

Glioblastoma multiforme (GBM) or “glioblastoma,” is the most common and aggressive malignant primary brain tumor in humans. An effective treatment that increases patient survival would represent a significant advance in the field, and provide a desperately needed new therapy for this deadly disease. Herein we disclose the identification of the target of the tumor homing peptide which, when conjugated to ‘nanoworms’, deliver and carry the pro-apoptotic nanoparticle system selectively to the tumor target tissue. This nanosystem has shown unprecedented anti-cancer activity in highly drug resistant/refractory mouse models of glioblastoma, which closely mimic the human disease and thus provide an exciting new opportunity for the treatment of GBM. Plans for further development of this Nanosystem will also be discussed.

Citation Format: Sarah Hudson, Lilach Agemy, Venkata Ramana Kotamraju, Shweta Sharma, Erkki Ruoslahti, Florence Brunel, Ann MacLaren, John Muraski, Deborah Slee. Targeted nanoparticle based therapy for the treatment of glioblastoma multiforme: Unprecedented anti-cancer activity in highly drug resistant/refractory mouse models of glioblastoma with novel apoptotic nanoparticles which hone to a cell-surface protein f [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5415. doi:10.1158/1538-7445.AM2014-5415
Abstract 5417: Improved tumor targeting by BLD1-ELP
Authors: Cho Eun-A , Sarangthem Vijaya Devi , Lee Byung-Heon , Kim In-San , Park Rang-Woon
Published: May 2015

Elastin-like polypeptide (ELP) is a promising class of recombinant biopolymers for drug delivery to solid tumors. It is a thermally responsive

polypeptide derived from mammalian elastin and consists of repeating pentapeptide sequence, Val-Pro-Gly-X-Gly, where X can be any amino acid except proline. ELPs conjugated to targeting peptide and drugs would enable enhanced targeting for drug delivery to solid tumors. BLD1 is a peptide which can selectively bind to bladder tumor cells. Not only for overcoming its rapid elimination from circulation and short half-life, but also enhancing tumor targeting efficiency, we introduced multiple BLD1 into the ELP (BLD1-ELP). Transition temperature (Tt) of BLD1-ELP was approximately 39 °C. BLD1-ELP showed superior cell binding ability than BLD1 peptide alone with 5637 and HT-1376 bladder tumor cell lines. The confocal microscopic imaging further confirmed that BLD1-ELP polymer efficiently bound to 5637 cells and HT-1376 cells compare to HEK293 embryonic kidney epithelial cells. The cellular uptake of BLD1-ELP was also much higher in 5637 cells and HT-1376 cells than in HT-29 colon cancer cells and HEK293 cells. In in vivo imaging analysis, tumor targeting of intravenously injected BLD1-ELP was observed in 5637 tumor xenograft model. These data suggest that BLD1-ELP can be developed as an effective tumor targeting, drug delivery system for diagnosis and therapy.

Citation Format: Eun-A Cho, Vijaya Devi Sarangthem, Byung-Heon Lee, In-San Kim, Rang-Woon Park. Improved tumor targeting by BLD1-ELP. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5417. doi:10.1158/1538-7445.AM2014-5417