mp39-20 aleatoric large dataset analysis framework: a practical approach to mining public expression...

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HSP90 inhibitor) as well as STA9090 and AUY922 (second genera- tion inhibitors). Cells were also treated with the HSP70 inhibitor VER 155008 alone and in combination with a HSP90 inhibitor. Cell prolif- eration rates were determined by MTT assays, while the expression of HSPs, apoptotic and cell signaling markers were determined by Western analysis. RESULTS: UMUC3 cells showed the most sensitivity of all cell lines. Fifty percent growth inhibition occurred within 48H of treatment using 10 nM of the second generation inhibitors. This same degree of inhibition required 10-fold higher concentrations of 17-AAG. STA9090 exhibited the highest efcacy showing 80% growth inhibition at 100 nM for all the cell lines tested. All cell lines showed a 5-10 fold increase in the expression of HSP70 within 24 H of treatment with HSP90 inhibitors. In addition there was also a 50% increase in the expression of HSP40, 60 and 110. Since the overexpression of other HSPs may compensate for the inhibition of HSP90, we sequentially inhibited the expression of HSP90 with STA9090, and HSP70 with VER 155008, and determined the effects on cell proliferation. The combination of drugs showed a synergistic inhibition of growth with 78% inhibition at 24H compared to 68% inhibition with VER155008 alone, or 43% inhibition with STA9090 alone. HSP90 inhibition induced apoptosis as demonstrated by increased expression of cleaved caspase 3 and downregulation of mediators of several oncogenic signaling pathways including EGFR, ErbB2, cyclin D1, pAKT, pSTAT3/5, pS6, p4EBP1 in the cell lines tested. CONCLUSIONS: HSP inhibitors as monotherapy have shown promising preclinical efcacy but this has not been replicated in clinical trials. Data from this study suggests that combination HSP90/70 inhibition is superior to either alone in a bladder cancer cytotoxicity model and the signicance of this in the clinical setting remains to be seen. Source of Funding: This work was supported by internal grant SRC-S-22 from the Geisinger Health System to HW. MP39-19 L-SELECTIN (CD62L) EXPRESSION IN HIGH GRADE UROTHELIAL CARCINOMA AS A POTENTIAL MARKER OF METASTATIC DISEASE Dharamainder Choudhary, Poornima Hegde, Shilpa Choudhary, Kevin Claffey, Pramod Srivastava, Carol Pilbeam, John Taylor III*, Farmington, CT INTRODUCTION AND OBJECTIVES: L-selectin (CD62L) is a vascular adhesion molecule constitutively expressed on leucocytes with a primary function of directing leucocyte migration and homing of lymphocytes to lymph nodes (LNs). Microarray data from laser captured, micro-dissected human specimens of high grade muscle invasive (MIBC) vs. low grade (LGBC) bladder cancers found CD62L to be the highest differentially expressed gene between the groups. We further characterized the mRNA and protein expression of CD62L in high grade cancer and its potential as a marker for metastatic disease. METHODS: MIBC and LGBC fresh frozen, parafn embedded and serum samples were obtained from the UCHC tumor bank. mRNA was evaluated by quantitative polymerase chain reaction (qPCR) and protein levels by immunohistochemistry (IHC) and enzyme linked immunosorbant assay (ELISA). Flow cytometry (FACS analysis) was used to identify the relative number of cells expressing CD62L in fresh tumor tissue. In silico studies were performed using the Onco- mine Database. RESULTS: Quantication of CD62L transcripts in high grade metastatic MIBC vs. LGBC frozen specimens(microarray; 3.81 2.94 vs 0.06 0.01 p¼0.04 ,conrmed by qPCR 0.14 0.04 vs. 23.31 22.47) and immunohistochemistry on parafn embedded high grade metastatic MIBC vs. LGBC specimens conrmed the elevated expression of CD62L in MIBC samples. Localization of CD62L was also conrmed in discrete foci of bladder tumor cells in LN specimens of high grade metastatic disease. Upregulated expression of CD62L (9.4-fold, p<0.01) was observed by FACS analysis of freshly isolated tumor cells from high grade cancers vs. LGBC specimens. Circulating CD62L levels were also found to be higher (640 75 vs. 558 34 ng/ml) in serum samples from pa- tients with high grade metastatic vs. high grade non-metastatic MIBC. Furthermore, in silico analysis using the Oncomine microarray database showed an association of CD62L expression with tumor aggressiveness and clinical outcomes. CONCLUSIONS: Our preliminary ndings are the rst report of increased expression of CD62L in MIBC and suggest a role in met- astatic spread to LNs. CD62L could act as a potential marker for pre- dicting patients who are at high risk of developing or harboring metastatic disease. Source of Funding: ACS-MRSG 08-270-01-CCE and The Leo and Anne Albert Charitable Trust (JAT), NIH R01DK48361(CCP) MP39-20 ALEATORIC LARGE DATASET ANALYSIS FRAMEWORK: A PRACTICAL APPROACH TO MINING PUBLIC EXPRESSION DATA FOR CANCER RESEARCHERS Jonathan A. Ewald*, Howard H. Bailey, William A. Ricke, Tracy M. Downs, Madison, WI INTRODUCTION AND OBJECTIVES: Public archives of expression microarray data provide a powerful resource for cancer research that can save valuable resources by allowing existing data to be re-purposed. These results from previous and current studies include data from in vitro experiments and analyses of clinical patient- derived tissues, including tumors. The availability of these data to the at- large cancer research community can promote the development of innovative ideas that otherwise may not occur to a professional data analyst. However, many investigators avoid this resource due to a perception that these data are inaccessible and too big for a cancer biologist or clinician to manage and interrogate effectively. Recent ad- vances in bioinformatics software development have produced open- access tools more friendly to use by the general population. Our objective was to develop a practical, versatile workow to guide cancer researchersuse of public expression microarray data for hypothesis development and validation. METHODS: In our experiences exploring and interrogating this resource, we have developed a simple, intuitive framework largely through trial-and-error to guide our selection, comparison, and analysis. RESULTS: This approach, called ALDAF (Aleatoric Large Dataset Analysis Framework), provides a rules-based needs-driven strategy that is adjustable and adaptable to diverse research goals. This includes: (1) Exploring and Identifying Datasets; (2) Calculating Differences; (3) Selecting Data: Top-Down; (4) Selecting Data: Bot- tom-Up; (5) Bioinformatics Analysis and Interpretation; and (6) Vali- dation of Selected Data. Data is available through the NCBI Gene Expression Omnibus (GEO), which can be searched according to keywords to identify applicable data. To compile, compare, identify and select data, we use Microsoft Excel to automate many of these tasks using formulas that simplify and accelerate this process. Resulting lists of genes can then be analyzed and interpreted using open-access web-based bioinformatics programs including Web- Gestalt, DAVID, Chilibot, and PubGene/Coremine. Gene lists can also be veried by iterative analysis of additional independent data- sets to further select genes of interest, or validated by novel original experiments. CONCLUSIONS: We conclude that ALDAF provides a simple, intuitive and practical means for cancer researchers to utilize public expression microarray data. Source of Funding: None Vol. 191, No. 4S, Supplement, Sunday, May 18, 2014 THE JOURNAL OF UROLOGY â e433

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Vol. 191, No. 4S, Supplement, Sunday, May 18, 2014 THE JOURNAL OF UROLOGY� e433

HSP90 inhibitor) as well as STA9090 and AUY922 (second genera-tion inhibitors). Cells were also treated with the HSP70 inhibitor VER155008 alone and in combination with a HSP90 inhibitor. Cell prolif-eration rates were determined by MTT assays, while the expressionof HSPs, apoptotic and cell signaling markers were determined byWestern analysis.

RESULTS: UMUC3 cells showed the most sensitivity of allcell lines. Fifty percent growth inhibition occurred within 48H oftreatment using 10 nM of the second generation inhibitors. Thissame degree of inhibition required 10-fold higher concentrations of17-AAG. STA9090 exhibited the highest efficacy showing 80%growth inhibition at 100 nM for all the cell lines tested. All cell linesshowed a 5-10 fold increase in the expression of HSP70 within 24H of treatment with HSP90 inhibitors. In addition there was also a50% increase in the expression of HSP40, 60 and 110. Since theoverexpression of other HSPs may compensate for the inhibition ofHSP90, we sequentially inhibited the expression of HSP90 withSTA9090, and HSP70 with VER 155008, and determined the effectson cell proliferation. The combination of drugs showed a synergisticinhibition of growth with 78% inhibition at 24H compared to 68%inhibition with VER155008 alone, or 43% inhibition with STA9090alone. HSP90 inhibition induced apoptosis as demonstrated byincreased expression of cleaved caspase 3 and downregulationof mediators of several oncogenic signaling pathways includingEGFR, ErbB2, cyclin D1, pAKT, pSTAT3/5, pS6, p4EBP1 in the celllines tested.

CONCLUSIONS: HSP inhibitors as monotherapy have shownpromising preclinical efficacy but this has not been replicated inclinical trials. Data from this study suggests that combinationHSP90/70 inhibition is superior to either alone in a bladder cancercytotoxicity model and the significance of this in the clinical settingremains to be seen.

Source of Funding: This work was supported by internal grantSRC-S-22 from the Geisinger Health System to HW.

MP39-19L-SELECTIN (CD62L) EXPRESSION IN HIGH GRADEUROTHELIAL CARCINOMA AS A POTENTIAL MARKER OFMETASTATIC DISEASE

Dharamainder Choudhary, Poornima Hegde, Shilpa Choudhary,Kevin Claffey, Pramod Srivastava, Carol Pilbeam, John Taylor III*,Farmington, CT

INTRODUCTION AND OBJECTIVES: L-selectin (CD62L) is avascular adhesion molecule constitutively expressed on leucocyteswith a primary function of directing leucocyte migration and homingof lymphocytes to lymph nodes (LNs). Microarray data from lasercaptured, micro-dissected human specimens of high grade muscleinvasive (MIBC) vs. low grade (LGBC) bladder cancers foundCD62L to be the highest differentially expressed gene between thegroups. We further characterized the mRNA and protein expressionof CD62L in high grade cancer and its potential as a marker formetastatic disease.

METHODS: MIBC and LGBC fresh frozen, paraffin embeddedand serum samples were obtained from the UCHC tumor bank. mRNAwas evaluated by quantitative polymerase chain reaction (qPCR) andprotein levels by immunohistochemistry (IHC) and enzyme linkedimmunosorbant assay (ELISA). Flow cytometry (FACS analysis) wasused to identify the relative number of cells expressing CD62L in freshtumor tissue. In silico studies were performed using the Onco-mine Database.

RESULTS: Quantification of CD62L transcripts in high grademetastatic MIBC vs. LGBC frozen specimens(microarray; 3.81 �2.94 vs 0.06 � 0.01 p¼0.04 ,confirmed by qPCR 0.14 � 0.04 vs.23.31 � 22.47) and immunohistochemistry on paraffin embeddedhigh grade metastatic MIBC vs. LGBC specimens confirmed theelevated expression of CD62L in MIBC samples. Localization of

CD62L was also confirmed in discrete foci of bladder tumor cells inLN specimens of high grade metastatic disease. Upregulatedexpression of CD62L (9.4-fold, p<0.01) was observed by FACSanalysis of freshly isolated tumor cells from high grade cancers vs.LGBC specimens. Circulating CD62L levels were also found to behigher (640 � 75 vs. 558 � 34 ng/ml) in serum samples from pa-tients with high grade metastatic vs. high grade non-metastaticMIBC. Furthermore, in silico analysis using the Oncomine microarraydatabase showed an association of CD62L expression with tumoraggressiveness and clinical outcomes.

CONCLUSIONS: Our preliminary findings are the first reportof increased expression of CD62L in MIBC and suggest a role in met-astatic spread to LNs. CD62L could act as a potential marker for pre-dicting patients who are at high risk of developing or harboringmetastatic disease.

Source of Funding: ACS-MRSG 08-270-01-CCE andThe Leo and Anne Albert Charitable Trust (JAT), NIHR01DK48361(CCP)

MP39-20ALEATORIC LARGE DATASET ANALYSIS FRAMEWORK:A PRACTICAL APPROACH TO MINING PUBLIC EXPRESSIONDATA FOR CANCER RESEARCHERS

Jonathan A. Ewald*, Howard H. Bailey, William A. Ricke,Tracy M. Downs, Madison, WI

INTRODUCTION AND OBJECTIVES: Public archives ofexpression microarray data provide a powerful resource for cancerresearch that can save valuable resources by allowing existing data tobe re-purposed. These results from previous and current studiesinclude data from in vitro experiments and analyses of clinical patient-derived tissues, including tumors. The availability of these data to the at-large cancer research community can promote the development ofinnovative ideas that otherwise may not occur to a professionaldata analyst. However, many investigators avoid this resource due to aperception that these data are inaccessible and too big for a cancerbiologist or clinician to manage and interrogate effectively. Recent ad-vances in bioinformatics software development have produced open-access tools more friendly to use by the general population. Ourobjective was to develop a practical, versatile workflow to guide cancerresearchers’ use of public expression microarray data for hypothesisdevelopment and validation.

METHODS: In our experiences exploring and interrogating thisresource, we have developed a simple, intuitive framework largelythrough trial-and-error to guide our selection, comparison, and analysis.

RESULTS: This approach, called ALDAF (Aleatoric LargeDataset Analysis Framework), provides a rules-based needs-drivenstrategy that is adjustable and adaptable to diverse research goals.This includes: (1) Exploring and Identifying Datasets; (2) CalculatingDifferences; (3) Selecting Data: Top-Down; (4) Selecting Data: Bot-tom-Up; (5) Bioinformatics Analysis and Interpretation; and (6) Vali-dation of Selected Data. Data is available through the NCBI GeneExpression Omnibus (GEO), which can be searched according tokeywords to identify applicable data. To compile, compare, identifyand select data, we use Microsoft Excel to automate many of thesetasks using formulas that simplify and accelerate this process.Resulting lists of genes can then be analyzed and interpreted usingopen-access web-based bioinformatics programs including Web-Gestalt, DAVID, Chilibot, and PubGene/Coremine. Gene lists canalso be verified by iterative analysis of additional independent data-sets to further select genes of interest, or validated by novel originalexperiments.

CONCLUSIONS: We conclude that ALDAF provides a simple,intuitive and practical means for cancer researchers to utilize publicexpression microarray data.

Source of Funding: None