bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1082: High-throughput,purification-free, multiplexed profiling of circulating miRNA for discovery,validation, and diagnostics
Authors: Tytell Jessica , Stoner Issac , Tackett Michael , Doran Graeme , Rafferty Conor , Windemuth Andreas , Pregibon Daniel 
Published: July 2016

Abstract
To address the needs for circulating miRNA biomarker validation, we developed the Multiplexed Circulating microRNA assay. This assay enables the detection of up to 68 microRNA targets per sample in 96-well format with readout on standard flow cytometers and analysis with an included bioinformatics software package. The Circulating microRNA assay combines particle-based multiplexing, using patented Firefly hydrogel particles, with single-step RT-PCR signal amplification using universal primers. Thus, the Circulating microRNA assay leverages PCR sensitivity while eliminating the need for separate reverse transcription reactions and mitigating amplification biases introduced by target-specific qPCR. Furthermore, the ability to multiplex targets in each well eliminates the need to split valuable samples into multiple reactions. Results from the Circulating microRNA assay are displayed and interpreted using our included Firefly Analysis Workbench, which allows visualization, normalization, and export of experimental data with only a few mouse clicks. To aid discovery and validation of biomarkers, we have generated fixed panels for Oncology, Cardiology, Neurology, Immunology, and Liver Toxicology. These carefully curated panels include hemolysis markers to assess sample quality, as well as critical normalization factors. Here we present the data from several studies investigating circulating and tumor microRNA profiles using the Firefly Circulating microRNA Assay Fixed Panels.
Together, this novel combination of bioinformatics tools and multiplexed, high-sensitivity assays enables rapid discovery and validation of microRNA biomarker signatures from fluid specimens.
Citation Format: Jessica Tytell, Issac Stoner, Michael Tackett, Graeme Doran, Conor Rafferty, Andreas Windemuth, Daniel Pregibon. High-throughput,purification-free, multiplexed profiling of circulating miRNA for discovery,validation, and diagnostics. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1082.
Abstract 1089: Cardiac glycosides affect miRNA expression profiles in renal cell carcinoma cell lines
Authors: Nolte Elke , Wach Sven , da Silva Izabella T. , Ekici Arif , Müller-Uri Frieder , Kreis Wolfgang , Vera-Gonzales Julio , Wullich Bernd , Taubert Helge , Lai Xin 
Published: July 2016

Abstract
Background: Renal Cell Carcinoma (RCC) is the ninth most common cancer worldwide, with about 338,000 new cases diagnosed in 2012. Especially metastatic renal cell carcinoma has still despite surgical cytoreduction, VEGF-tyrosine kinase inhibitors, mTOR inhibitors and first promising results of immunotherapies a very poor prognosis what implies an urgent need for additional therapies. Cardiac glycosides have come into the focus as potential cancer treatment option. They can have anti-proliferative and apoptotic characteristics in several cancer cell lines but affect only in a much lesser extent normal cell lines. MicroRNAs are small non-coding RNAs of 17-25 nucleotides length that widely exist and they play an important regulating role in many normal and pathophysiological cellular processes, as cell proliferation, differentiation, induction of apoptosis, tumorigenesis and tumor progression.
Material and Methods: Four renal cell carcinoma cell lines were treated with three different cardiac glycosides in the IC50 concentrations during 72h. For the investigation of miRNA expression miRNA microarray expression analyses were performed. In silico target gene and pathway enrichment analyses were performed.
Results: An overlap between all treatments and all cell lines could be detected for two mature miRNAs and two premature miRNAs. Pathway enrichment analysis identified MAPK and axon guidance pathways. Moreover, we looked for genes predicted to be regulated by the deregulated miRNAs in all cell lines at all treatments in the MAPK and the axon guidance pathways.
Conclusion: The identification and characterization of deregulated miRNAs after cardiac glycoside treatment could give insight in their gene regulation and thus help to clarify the molecular basis of their anti-proliferative and apoptotic effects.
Citation Format: Elke Nolte, Sven Wach, Izabella T. da Silva, Arif Ekici, Frieder Müller-Uri, Wolfgang Kreis, Julio Vera-Gonzales, Bernd Wullich, Helge Taubert, Xin Lai. Cardiac glycosides affect miRNA expression profiles in renal cell carcinoma cell lines. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1089.
Abstract 1090: microRNA regulation of Nrf2 and the antioxidant response in breast cancer cells following redox therapy
Authors: Mascia Francesca , Pokrzywinski Kaytee L. , Rao. V. Ashutosh 
Published: July 2016

Abstract
Mitoquinone (MitoQ), a redox-active mitochondrially targeted chemotherapy, activates autophagy through the production of reactive oxygen species (ROS) in breast cancer cells. Studies have also shown a concomitant activation of Nrf2 and the antioxidant response with MitoQ treatment. Nrf2 (nuclear factor (erythroid-derived 2)-like 2) is a transcription factor that regulates the antioxidant response element. Drugs that stimulate Nrf2 are ideal for the treatment of diseases induced by oxidative stress; however, over-activation of Nrf2 may promote tumor growth and diminish the effects of redox active chemotherapies. Therefore, understanding the relationship between autophagy and oxidative stress is crucial for determining the fate of cancer cells exposed to redox-active oncology agents. The aim of this study was to evaluate microRNA (miRNA) as a link between oxidative stress and autophagy through modulation of Nrf2 activity. microRNA are endogenous small (18-22 base pairs long) double stranded RNA that bind to the 3’ UTR of target mRNA. miRNA function through translational repression via mRNA recycling and degradation. To this aim we set out on finding miRNA that suppress the antioxidant response, modulated by Nrf2, in cancer cells after redox therapy with the goal of inducing a death response. After 24 hours of non-target pool or Nrf2 silencing, using small interfering RNAs, MDA-MB-231 cells were treated with DMSO or MitoQ for 18 hours. RNA was extracted and miRNAs were identified using Illumina RNA sequencing. DEseq revealed 97 miRNAs that were differentially expressed at α &lt; 0.05. Biologically significant miRNAs were then distinguished by using a Log2 fold change cut off of -1.0 &lt; and &lt; 1.0, which identified 39 microRNAs. Since miRNA should be high when their target is low we were predominantly interested in the 15 miRNAs that were down-regulated (DMSO:MitoQ). 7 of the 15 down-regulated miRNAs were also down-regulated in the presence of Nrf2 silencing in both the DMSO and MitoQ treatments. We are currently investigating these 7 miRNAs in terms of the specific effect they have on the Nrf2 pathway during redox therapy.
Citation Format: Francesca Mascia, Kaytee L. Pokrzywinski, V. Ashutosh Rao. microRNA regulation of Nrf2 and the antioxidant response in breast cancer cells following redox therapy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1090.
Abstract 1093: The melanoma-enriched microRNA miR-4731 regulates genes involved in cell cycle and the melanosome
Authors: Stark Mitchell S. , Tom Lisa , Boyle Glen M. , Bonazzi Vanessa F. , Herington Adrian C. , Pollock Pamela M. , Hayward Nicholas K. 
Published: July 2016

Abstract
We previously identified miR-4731-5p (miR-4731) as a melanoma-enriched microRNA following comparison of melanoma with other cell lines from solid malignancies. Additionally, miR-4731 has been found in serum from melanoma patients and expressed less abundantly in metastatic melanomas from stage IV patients relative to stage III patients. As miR-4731 has no known function, we used biotin-labelled miRNA duplex pull-down to identify binding targets of miR-4731 in three melanoma cell lines. Using the miRanda miRNA binding algorithm, all pulled-down transcripts common to the three cell lines (n = 1092) were predicted to be targets of miR-4731 and gene-set enrichment analysis of these (via STRING v9.1) highlighted significantly associated genes related to the ‘cell cycle’ and ‘melanosome’ pathways. Following miR-4731 overexpression, a selection (n = 81) of pull-down transcripts underwent validation using a custom qRT-PCR array. These data revealed that miR-4731 regulates multiple genes associated with the cell cycle (e.g. CCNA2, ORC5L, and PCNA) and melanosome (e.g. RAB7A, CTSD, and GNA13). Furthermore, members of the synovial sarcoma X breakpoint family (SSX) (melanoma growth promoters) were also down-regulated (e.g. SSX2, SSX4, and SSX4B) as result of miR-4731 overexpression. We therefore speculate that loss of miR-4731 expression supports melanoma growth by, in part; reducing its regulatory control of SSX expression levels together with members of the cell cycle pathway, which warrants further investigation.
Citation Format: Mitchell S. Stark, Lisa Tom, Glen M. Boyle, Vanessa F. Bonazzi, Adrian C. Herington, Pamela M. Pollock, Nicholas K. Hayward. The melanoma-enriched microRNA miR-4731 regulates genes involved in cell cycle and the melanosome. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1093.
Abstract 1096: microRNA-193a-3p acts as a tumor suppressor in BRAF-mutated colorectal cancer
Authors: Takahashi Hidekazu , Takahashi Masanobu , Takahashi Shin , Shimodaira Hideki , Ishioka Chikashi 
Published: July 2016

Abstract
The aim of this study was to identify microRNAs (miRNAs) specifically dysregulated in BRAF-mutant colorectal cancer, a malignant subtype of colorectal cancer. The genome-wide miRNA expression analysis in a screening set (n = 30) identified 22 miRNAs specifically dysregulated in BRAF-mutant cancers. Among the top 5 dysregulated miRNAs, the validation analysis using another set of patients (n = 34) confirmed miR-31 and miR-135b as significantly up-regulated miRNAs and miR-193a-3p as a significantly down-regulated one. Moreover, functional assays supported its tumor-suppressive role in colorectal cancer. Finally, the expression status of miR-193a-3p correlated with clinical outcome of patients treated with anti-EGFR antibodies. Taken together, these results show a novel functional role of miR-193a-3p as a tumor suppressive miRNA in colorectal cancer, particularly with BRAF mutations. Further studies are needed to clarify the precise molecular mechanisms as to how this miRNA is involved in colorectal tumorigenesis, which could help further develop a therapeutic strategy for colorectal cancer.
Citation Format: Hidekazu Takahashi, Masanobu Takahashi, Shin Takahashi, Hideki Shimodaira, Chikashi Ishioka. microRNA-193a-3p acts as a tumor suppressor in BRAF-mutated colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1096.
Abstract 1097: The miR-17-92 microRNA cluster plays a crucial role in osteosarcoma progression
Authors: Varshney Jyotika , Slipek Nicholas J. , Osborne John , Chang Adrian , Sarver Anne E. , Cornax Ingrid , O’Sullivan Gerry M. , Subramanian Subbaya , Largaespada David A. 
Published: July 2016

Abstract
Osteosarcoma is the most common primary bone malignancy that affects adolescents. Around 30% of patients with localized osteosarcoma and 70% of patients with metastasis will experience treatment failure within 5 years of diagnosis. The complex biology of osteosarcoma and astounding genetic heterogeneity has made it challenging to identify effective new gene targets and therapeutic agents. Our studies found an overall overexpression of a microRNA cluster, miR-17-92 microRNAs in human primary osteosarcoma compared to normal bone. We learned that upregulation of this miR-17-92 cluster simultaneously silences a suite of key tumor suppressors. Using data from a novel spontaneous osteosarcoma mouse model and genetic screen, we discovered miR-17-92 targets, such as PTEN, PTRPD and SRGAP2, which are potential tumor suppressor genes. Specifically blocking miR-17-92 function in osteosarcoma cells reduced their migration and ability to grow larger tumors in immunodeficient mice compared to the controls. Also, knockdown of miR-17-92 cluster microRNAs led to increase in the levels of PTPRD and SRGAP2 in cells as well as tumors; further suggesting that miR-17-92 is targeting these genes. We also performed gain-of-function of miR-17-92 studies in a poorly aggressive osteosarcoma cell line and found that overexpression of miR-17-92 leads to ability to grow in an anchorage independent manner and form tumors in immunodeficient mice, both features that are lacking in the parental line. Ongoing RNA sequencing studies on miR-17-92 target transcripts in osteosarcoma cells, and functional analyses of miR-17-92 deletion mutants, will be presented. In an attempt to target miR-17-92 miRNA expression, we have tested small molecules. Our data suggests that triptolide, a diterpenoid epoxide, inhibits MYC expression and downregulates miR-17-92 miRNAs resulting in upregulation of several tumor suppressor driver proteins including PTEN, PTPRD, and SRGAP2. Together, our data suggests that upregulation of miR-17-92 miRNAs contributes to osteosarcoma progression and triptolide inhibits miR-17-92 expression. These data have implications for how sarcomas develop in general and suggest a new way to treat cancer by targeting microRNAs using small molecules.
Citation Format: Jyotika Varshney, Nicholas J. Slipek, John Osborne, Adrian Chang, Anne E. Sarver, Ingrid Cornax, Gerry M. O’ Sullivan, Subbaya Subramanian, David A. Largaespada. The miR-17-92 microRNA cluster plays a crucial role in osteosarcoma progression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1097.
Abstract 1115: Serum miR152 as a novel prognostic biomarker and potential tumor suppressor for early stage non-small cell lung cancer
Authors: Oba Taro , Ye Yuanqing , Zhang Liren , Lin Jing , Gentile Emanuela , Wang Jing , Zhao Yang , Gu Jiang , Wistuba Ignacio , Roth Jack A. , Wu Xifeng , Ji Lin 
Published: July 2016

Abstract
Cancer-derived circulating miRNAs represent a promising new class of circulating biomarkers for cancer detection, prognosis, and therapeutic targets. We analyzed the differential c-miRNA expression levels of ∼100 candidate serum miRNAs by quantitative RT-PCR in 174 Caucasian, early stage lung cancer patients and 184 Caucasian healthy controls. Serum miR152 exhibited significant differential expression between cases and controls (P = 0.014). Low levels of serum miR152 expression were consistently associated with an increased risk of lung cancer. The down-regulated miR152 expression was also detected across a panel of 40 NSCLC and normal bronchial epithelial cell lines and in 250 primary tumors by miRNA expression profiling on microarrays. The tumor-derived origin of the c-miR150 was confirmed by an increased level of serum miR152 with increased tumor volumes three weeks after tumor cell inoculation in a human H1299 tumor xenograft mouse model by qRT-PCR assay. Ectopic expression of miR-152 suppressed tumor cell proliferation, colony formation, and cell migration/invasion in NSCLC H1299, H460, and A549 cells transfected by miR-152 expression plasmids. Inhibition of miR-152 expression by a miR-152 inhibitor promoted tumor cell proliferation in HCC15 cells. Overexpression of miR152 in H1299, H460 and A549 cells significantly down-regulated the constitutive expression of the DNMT1 miR-152 target gene and protein, suggesting its potential role in the epigenetic regulation of lung cancer pathogenesis. These results suggest that serum miR-152 may serve as a novel negative predictor for lung cancer risk, recurrence, and survival in early stage NSCLC and function as a potential tumor suppressor miRNA by epigenetic down-regulation of oncogenesis.(This study is partially supported by NIH/NCI grants Lung SPORE 5P50CA070907 and R01CA176568, a CPRIT Grant and a MDACC Moonshot Program Grant)
Citation Format: Taro Oba, Yuanqing Ye, Liren Zhang, Jing Lin, Emanuela Gentile, Jing Wang, Yang Zhao, Jiang Gu, Ignacio Wistuba, Jack A. Roth, Xifeng Wu, Lin Ji. Serum miR152 as a novel prognostic biomarker and potential tumor suppressor for early stage non-small cell lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1115.
Abstract 1116: Contribution of miR-199a to subtype switching of the SW13 adrenocortical carcinoma cell line
Authors: Gerona Tracy , Davis McKale , Hull Elizabeth 
Published: July 2016

Abstract
The human adrenocortical carcinoma SW13 cell line has two subtypes that are phenotypically distinct. The SW13- subtype is highly proliferative and epithelial-like, while the SW13+ subtype is slow growing, motile, and mesenchymal-like. These differences are mediated in part by the post-transcriptional regulation of BRM, which is expressed in SW13+ cells, and not detectable in SW13- cells. While treatment with histone deacetylase inhibitors (HDACi) can force cells to transition from SW13- to SW13+, the epigenetic mechanisms involved in the subtype switch are unknown. Recently, it was shown that miR-199a is a potent negative regulator of BRM expression in many epithelial tumor cell lines. Given this, we examined the expression of miR-199a in the two SW13 subtypes, and indeed found that miR-199a expression was significantly higher in the BRM-deficient SW13- cells than the BRM-expressing SW13+ cells. To begin to further assess the involvement of miR-199a in the SW13 subtype switch, SW13+ and SW13- cells were treated with either a miR-199a mimic or miR-199a inhibitor, respectively and assessed for differences in BRM mRNA and protein expression, as well changes in cell-type morphology. Our results indicate that although miR-199a can mediate differences in BRM expression, miR-199a alone is not sufficient to induce a full subtype conversion as evidenced by retention of subtype morphology following miR-199a inhibition and over-expression. We are currently investigating the role of miR-199a in HDACi mediated subtype conversion, as well as the expression of other miRNA and their targets that are differentially expressed between the two SW13 subtypes.
Citation Format: Tracy Gerona, McKale Davis, Elizabeth Hull. Contribution of miR-199a to subtype switching of the SW13 adrenocortical carcinoma cell line. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1116.
Abstract 1121: Validation of FOXR2 and ARHGAP36 as oncogenes in medulloblastoma
Authors: Jackson Pauline , Larsson Alex , Das Paramita , Largaespada David 
Published: July 2016

Abstract
We are working to validate two putative oncogenes in medulloblastoma (MB), ARHGAP36 and FOXR2. These genes were identified as MB drivers using a Sleeping Beauty mutagenesis screen in mice and are overexpressed in subsets of human MB. We are using gain (GOF) and loss of function (LOF) studies both in vitro and in vivo to understand the roles of FOXR2 and ARHGAP36 in MB genesis. In GOF studies, both genes individually drove anchorage independent growth in a mouse cerebellar progenitor cell line (C17.2) and a human MB cell line (ONS76). When overexpressed individually in C17.2 cells, both FOXR2 and ARHGAP36 drove tumor formation in the flank of NU/J mice. We are also using an orthotopic injection model with C17.2 cells overexpressing either ARHGAP36 or FOXR2 individually to determine if these genes drive tumor formation in a more relevant setting. RNA sequencing and reverse-phase protein array analyses were also performed on WT and C17 cells overexpressing each oncogene to identify their effects in an unbiased manner. We are working to validate those effects using RT-PCR and Western analysis. In LOF studies, the CRISPR/Cas system is being used to create mutations in either the ARHGAP36 or FOXR2 locus in human MB cell lines (ONS76, MED8A, Daoy). This has been accomplished with ARHGAP36 in ONS76 cells, and we are currently characterizing those cells using proliferation, soft agar colony formation, and tumor formation assays. Lastly, we are working to create GOF and LOF mouse models of both FOXR2 and ARHGAP36 to characterize their oncogenic potential in vivo. We identified ARHGAP36 and FOXR2 as putative oncogenes in MB and our findings may elucidate novel targets for therapeutic efforts aimed at treating patients with MB.
Citation Format: Pauline Jackson, Alex Larsson, Paramita Das, David Largaespada. Validation of FOXR2 and ARHGAP36 as oncogenes in medulloblastoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1121.
Abstract 1122: FGFR1 can act as an oncogene or a tumor suppressor depending on the molecular context
Authors: Quintanal-Villalonga Álvaro , Ojeda-Márquez Laura , Marrugal Ángela , Suárez Rocío , Ferrer Irene , Carnero Amancio , Molina-Pinelo Sonia , Paz-Ares Luis 
Published: July 2016

Abstract
FGFR family of proteins has been extensively related to oncogenic properties in several types of tumors, including lung cancer. Among its members, FGFR1 has been related to squamous cell lung carcinoma, where FGFR1 amplification is present in 20% of patients. However, its role in lung cancer has not yet been thoroughly described.
Several lung cancer cell lines with different genetic backgrounds were transfected with plasmids to either overexpress or silence FGFR1. Then several tumorigenic abilities were tested in vitro and in vivo. mRNA from Paraffin-embedded tissue of a cohort of lung cancer patients was extracted and FGFR1 expression levels were measured and related to clinical characteristics.
FGFR1 increases oncogenic properties in SCC cell lines, but exerts anti-oncogenic effects in several lung ADC cell lines, suggesting a tumor suppressor role under certain circumstances. This is a consequence of differentially expressed genes among these two histologies. According to this, analysis of FGFR1 mRNA expression of a cohort of lung cancer patients revealed that high FGFR1 mRNA expression was associated to a shorter overall survival (OS) and progression free survival (PFS) in lung SCC patients. However, a trend for longer OS was observed for the ADC patients with higher FGFR1 mRNA expression.
FGFR1 has the potential to be either a tumor suppressor or an oncogene and the molecular context is a determining factor to define its final role in tumorigenesis.
Citation Format: Álvaro Quintanal-Villalonga, Laura Ojeda-Márquez, Ángela Marrugal, Rocío Suárez, Irene Ferrer, Amancio Carnero, Sonia Molina-Pinelo, Luis Paz-Ares. FGFR1 can act as an oncogene or a tumor suppressor depending on the molecular context. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1122.