29 results on '"Wach, S"'
Search Results
2. Heterogeneity-analysis of molecular subtypes of muscle-invasive bladder cancer and their precursor lesions in multiregion mapped whole-organ bladders
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Weyerer, V., primary, Lange, F., additional, Wullweber, A., additional, Stoehr, R., additional, Bertz, S., additional, Wach, S., additional, Taubert, H., additional, Wullich, B., additional, Sikic, D., additional, Strissel, P., additional, Strick, R., additional, Hartmann, A., additional, and Eckstein, M., additional
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- 2021
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3. Bladder tumor subtype commitment occurs in carcinoma in-situ driven by key signaling pathways including ECM remodeling
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Wullweber, A., primary, Strick, R., additional, Lange, F., additional, Sikic, D., additional, Taubert, H., additional, Wach, S., additional, Wullich, B., additional, Bertz, S., additional, Weyerer, V., additional, Stöhr, R., additional, Breyer, J., additional, Burger, M., additional, Hartmann, A., additional, Strissel, P., additional, and Eckstein, M., additional
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- 2021
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4. Heterogeneity-analysis of molecular subtypes of muscle-invasive bladder cancer and their precursor lesions in multiregion mapped whole-organ bladders
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Weyerer, V, primary, Lange, F, additional, Wullweber, A, additional, Stöhr, R, additional, Bertz, S, additional, Wach, S, additional, Taubert, H, additional, Wullich, B, additional, Sikic, D, additional, Strissel, P, additional, Strick, R, additional, Hartmann, A, additional, and Eckstein, M, additional
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- 2020
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5. Divergent immunobiological correlates of FDA-/EMA-approved PD-L1 assays and scoring algorithms in muscle-invasive bladder cancer
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Weyerer, V, primary, Geppert, CI, additional, Bertz, S, additional, Taubert, H, additional, Breyer, J, additional, Bolenz, C, additional, Erben, P, additional, Wach, S, additional, Sikic, D, additional, Kunath, F, additional, Wullich, B, additional, Hartmann, A, additional, and Eckstein, M, additional
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- 2020
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6. Prognostic role of FGFR alterations and FGFR mRNA expression in metastatic urothelial cancer treated with anti-PD(L1) inhibitors in first and second line setting
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Roghmann, F., primary, Wirtz, R., additional, Santiago-Walker, A., additional, Jarczyk, J., additional, Kriegmair, M.C., additional, Worst, T.S., additional, Sikic, D., additional, Wach, S., additional, Taubert, H., additional, Weyerer, V., additional, Stoehr, R., additional, Tully, K., additional, Zengerling, F., additional, Bolenz, C., additional, Breyer, J., additional, Burger, M., additional, Porubsky, S., additional, Hartmann, A., additional, Erben, P., additional, Eckstein, M., additional, and Jütte, H., additional
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- 2020
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7. Comparative analysis of tumour mutational burden (TMB) prediction methods and its association with determinants of the tumour immune microenvironment of urothelial bladder cancer (UBC)
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Eckstein, M., primary, Hartmann, A., additional, Strissel, P., additional, Strick, R., additional, Wach, S., additional, Taubert, H., additional, Wullich, B., additional, Geppert, C., additional, Weyerer, V., additional, Stoehr, R., additional, Rübner, M., additional, Fasching, P.A., additional, Rabizadeh, S., additional, Benz, S., additional, Haller, F., additional, Moskalev, E., additional, and Toegel, L., additional
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- 2019
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8. Prognostic role of FGFR Mutations and FGFR mRNA expression in metastatic urothelial cancer treated with anti-PD(L1) inhibitors in first and second-line setting
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Roghmann, F., primary, Wirtz, R., additional, Jarczyk, J., additional, Kriegmair, M.C., additional, Worst, T.S., additional, Sikic, D., additional, Wach, S., additional, Taubert, H., additional, Wullich, B., additional, Weyerer, V., additional, Stoehr, R., additional, Zengerling, F., additional, Bolenz, C., additional, Breyer, J., additional, Burger, M., additional, Porubsky, S., additional, Hartmann, A., additional, Erben, P., additional, Eckstein, M., additional, and Juette, H., additional
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- 2019
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9. Efficacy of anti-PD(L)1 treatment in patients with metastatic urothelial cancer based on mRNA- and protein- based PD-L1 determination: Results from the multicentric, retrospective FOsMIC trial
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Jarczyk, J., primary, Wirtz, R., additional, Roghmann, F., additional, Juette, H., additional, Kriegmair, M.C., additional, Worst, T.S., additional, Sikic, D., additional, Wach, S., additional, Taubert, H., additional, Wullich, B., additional, Weyerer, V., additional, Stoehr, R., additional, Zengerling, F., additional, Bolenz, C., additional, Breyer, J., additional, Burger, M., additional, Porubsky, S., additional, Hartmann, A., additional, Erben, P., additional, and Eckstein, M., additional
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- 2019
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10. Tumor immune microenvironment drives prognostic relevance correlating with bladder cancer subtypes
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Strissel, P., primary, Pfannstiel, C., additional, Chiappinelli, K., additional, Sikic, D., additional, Wach, S., additional, Wirtz, R., additional, Wullweber, A., additional, Taubert, H., additional, Breyer, J., additional, Otto, W., additional, Worst, T., additional, Burger, M., additional, Wullich, B., additional, Bolenz, C., additional, Fuhrich, N., additional, Geppert, C., additional, Stoehr, R., additional, Bertz, S., additional, Keck, B., additional, Erlmeier, F., additional, Erben, P., additional, Hartmann, A., additional, Strick, R., additional, and Eckstein, M., additional
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- 2019
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11. Cytotoxic T cell related gene expression signature predicts improved outcome in muscle-invasive urothelial bladder cancer patients following radical cystectomy and adjuvant chemotherapy
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Eckstein, M., primary, Wirtz, R., additional, Strissel, P., additional, Pfannstiel, C., additional, Wullweber, A., additional, Lange, F., additional, Erben, P., additional, Stoehr, R., additional, Bertz, S., additional, Geppert, C., additional, Fuhrich, N., additional, Weyerer, V., additional, Taubert, H., additional, Erlmeier, F., additional, Breyer, J., additional, Otto, W., additional, Keck, B., additional, Wach, S., additional, Kunath, F., additional, Strick, R., additional, Hartmann, A., additional, Wullich, B., additional, and Sikic, D., additional
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- 2019
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12. Performance of FDA/EMA approved PD-L1 assays in urothelial carcinoma with emphasis on therapy stratification for first-line use of atezolizumab and pembrolizumab
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Eckstein, M., primary, Erben, P., additional, Kriegmair, M., additional, Worst, T., additional, Weiß, C-A., additional, Wirtz, R., additional, Wach, S., additional, Stoehr, R., additional, Sikic, D., additional, Geppert, C., additional, Weyerer, V., additional, Bertz, S., additional, Breyer, J., additional, Otto, W., additional, Keck, B., additional, Burger, M., additional, Taubert, H., additional, Weichert, W., additional, Wullich, B., additional, Bolenz, C., additional, Hartmann, A., additional, and Erlmeier, F., additional
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- 2019
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13. Androgen receptor mRNA expression in urothelial carcinoma of the bladder: A retrospective analysis of two independent cohorts
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Sikic, D., primary, Wirtz, R.M., additional, Wach, S., additional, Dyrskjøt, L., additional, Erben, P., additional, Bolenz, C., additional, Breyer, J., additional, Otto, W., additional, Hoadley, K.A., additional, Lerner, S.P., additional, Eckstein, M., additional, Hartmann, A., additional, and Keck, B., additional
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- 2019
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14. Prognostic impact of tumor infiltrating lymphocytes and immune cell related gene expression after radical cystectomy in muscle-invasive bladder cancer
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Eckstein, M., primary, Pfannstil, C., additional, Wach, S., additional, Erben, P., additional, Sikic, D., additional, Wirtz, R., additional, Eidt, S., additional, Taubert, H., additional, Breyer, J., additional, Otto, W., additional, Burger, M., additional, Bertz, S., additional, Geppert, C., additional, Bolenz, C., additional, Worst, T.S., additional, Wullich, B., additional, Keck, B., additional, Robert, S., additional, and Hartmann, A., additional
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- 2018
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15. Old patient, bad outcome? Prospective evaluation of preoperative assessments as predictors of outcome and functional recovery after major urologic tumour surgery. First results of a prospective single centre study
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Kahlmeyer, A., primary, Losensky, W., additional, Brammertz, L., additional, Taubert, H., additional, Wach, S., additional, Keck, B., additional, Ritt, M., additional, Gassmann, K.G., additional, and Wullich, B., additional
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- 2017
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16. Serum miRNA-supported transrectal MRI-ultrasound fusion-guided biopsy of the prostate enhances tumor prediction and classification
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Keck, B., primary, Wach, S., additional, Pöllmann, J., additional, Jansen, T., additional, Kahlmeyer, A., additional, Taubert, H., additional, and Wullich, B., additional
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- 2017
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17. Prognostic impact of a 12-gene progression score in non-muscle invasive bladder cancer: A prospective multicenter validation study
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Dyrskjøt, L., primary, Reinert, T., additional, Algaba, F., additional, Christensen, E., additional, Nieboer, D., additional, Hermann, G., additional, Morgensen, K., additional, Marquez, M., additional, Segersten, U., additional, Hoyer, S., additional, Ulhøj, B., additional, Hartmann, A., additional, Stöhr, R., additional, Wach, S., additional, Nawroth, R., additional, Beukers, W., additional, Schwamborn, K., additional, Tulic, C., additional, Simic, T., additional, Junker, K., additional, Harving, N., additional, Petersen, A.C., additional, Jensen, J.B., additional, Keck, B., additional, Horstmann, M., additional, Maurer, T., additional, Steyerberg, E., additional, Zwarthoff, E., additional, Real, F., additional, Malats, N., additional, Malmström, P.-U., additional, and Ørntoft, T.F., additional
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- 2017
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18. 785 Neuropilin-2 and VEGF-C are independent prognostic factors for bladder cancer patients treated with transurethral resection and radiochemotherapy
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Keck, B., primary, Wach, S., additional, Taubert, H., additional, Ott, O.J., additional, Kunath, F., additional, Hartmann, A., additional, Bertz, S., additional, Zeiler, S., additional, Weiss, C., additional, Hönscheid, P., additional, Rödel, C., additional, Baretton, G.B., additional, Sauer, R., additional, Fietkau, R., additional, Wullich, B., additional, Krause, F.S., additional, Kausthubh, D., additional, and Muders, M.H., additional
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- 2014
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19. 868 Histologic subtypes of bladder cancer influence overall survival of patients treated by radical cystectomy and adjuvant cisplatin-based chemotherapy
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Keck, B., primary, Taubert, H., additional, Wach, S., additional, Stoehr, R., additional, Kunath, F., additional, Bertz, S., additional, Lehmann, J., additional, Stöckle, M., additional, Hartmann, A., additional, and Wullich, B., additional
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- 2012
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20. The new EYE-D™ dosemeter for measurements of HP(3) for medical staff
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Bilski, P., primary, Bordy, J.-M., additional, Daures, J., additional, Denoziere, M., additional, Fantuzzi, E., additional, Ferrari, P., additional, Gualdrini, G., additional, Kopeć, M., additional, Mariotti, F., additional, Monteventi, F., additional, and Wach, S., additional
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- 2011
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21. A new cylindrical phantom for eye lens dosimetry development
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Gualdrini, G., primary, Mariotti, F., additional, Wach, S., additional, Bilski, P., additional, Denoziere, M., additional, Daures, J., additional, Bordy, J.-M., additional, Ferrari, P., additional, Monteventi, F., additional, Fantuzzi, E., additional, and Vanhavere, F., additional
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- 2011
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22. Evaluation of dose area product vs. patient dose in diagnostic X-ray units
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Kisielewicz, K., primary, Truszkiewicz, A., additional, Wach, S., additional, and Wasilewska–Radwańska, M., additional
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- 2011
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23. 599 REGULATORY MECHANISMS OF E-CADHERIN LOSS IN PLASMACYTOID UROTHELIAL CARCINOMA
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Keck, B., primary, Stoehr, R., additional, Rogler, A., additional, Giedl, J., additional, Wach, S., additional, Becker, K.F., additional, Wullich, B., additional, and Hartmann, A., additional
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- 2011
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24. 628 MICRORNAS ARE REPRODUCIBLY DEREGULATED IN PROSTATE CARCINOMA AND ARE POTENTIAL REGULATORS OF SIGNAL TRANSDUCTION PATHWAYS LIKE PI3-KINASE OR MAP-KINASE PATHWAYS
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Wach, S., primary, Nolte, E., additional, Szczyrba, J., additional, Stöhr, R., additional, Hartmann, A., additional, Ørntoft, T., additional, Dyrskjøt, L., additional, Eltze, E., additional, Wieland, W., additional, Grässer, F., additional, and Wullich, B., additional
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- 2011
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25. 923 PLASMACYTOID UROTHELIAL CARCINOMA: RARE VARIANT OF AGGRESSIVE UROTHELIAL CARCINOMA
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Keck, B., primary, Stoehr, R., additional, Wach, S., additional, Rogler, A., additional, Fritsche, H.M., additional, Lehmann, J., additional, Wullich, B., additional, and Hartmann, A., additional
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- 2010
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26. The diffusion of hydrogen through pure iron membranes
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Wach, S., primary, Miodownik, A.P., additional, and Mackowiak, J., additional
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- 1966
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27. The diffusion and permeation of H through pure Fe membranes
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Wach, S., primary and Miodownik, A.P., additional
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- 1968
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28. The Immune Landscape of Cancer
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Vésteinn Thorsson, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, Galen F. Gao, Christopher L. Plaisier, James A. Eddy, Elad Ziv, Aedin C. Culhane, Evan O. Paull, I.K. Ashok Sivakumar, Andrew J. Gentles, Raunaq Malhotra, Farshad Farshidfar, Antonio Colaprico, Joel S. Parker, Lisle E. Mose, Nam Sy Vo, Jianfang Liu, Yuexin Liu, Janet Rader, Varsha Dhankani, Sheila M. Reynolds, Reanne Bowlby, Andrea Califano, Andrew D. Cherniack, Dimitris Anastassiou, Davide Bedognetti, Younes Mokrab, Aaron M. Newman, Arvind Rao, Ken Chen, Alexander Krasnitz, Hai Hu, Tathiane M. Malta, Houtan Noushmehr, Chandra Sekhar Pedamallu, Susan Bullman, Akinyemi I. Ojesina, Andrew Lamb, Wanding Zhou, Hui Shen, Toni K. Choueiri, John N. Weinstein, Justin Guinney, Joel Saltz, Robert A. Holt, Charles S. Rabkin, Alexander J. Lazar, Jonathan S. Serody, Elizabeth G. Demicco, Mary L. Disis, Benjamin G. Vincent, Ilya Shmulevich, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Michael Miller, Sheila Reynolds, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Michael Ryan, Jing Wang, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Carrie Cibulskis, Stacey B. Gabriel, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Li Ding, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, onathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. Pinto, Mark Schiffman, Laura S. Schmidt, Cathy D. Vocke, Nicolas Wentzensen, Robert Worrell, Hannah Yang, Marc Moncrieff, Chandra Goparaju, Jonathan Melamed, Harvey Pass, Natalia Botnariuc, Irina Caraman, Mircea Cernat, Inga Chemencedji, Adrian Clipca, Serghei Doruc, Ghenadie Gorincioi, Sergiu Mura, Maria Pirtac, Irina Stancul, Diana Tcaciuc, Monique Albert, Iakovina Alexopoulou, Angel Arnaout, John Bartlett, Jay Engel, Sebastien Gilbert, Jeremy Parfitt, Harman Sekhon, George Thomas, Doris M. Rassl, Robert C. Rintoul, Carlo Bifulco, Raina Tamakawa, Walter Urba, Nicholas Hayward, Henri Timmers, Anna Antenucci, Francesco Facciolo, Gianluca Grazi, Mirella Marino, Roberta Merola, Ronald de Krijger, Anne-Paule Gimenez-Roqueplo, Alain Piché, Simone Chevalier, Ginette McKercher, Kivanc Birsoy, Gene Barnett, Cathy Brewer, Carol Farver, Theresa Naska, Nathan A. Pennell, Daniel Raymond, Cathy Schilero, Kathy Smolenski, Felicia Williams, Carl Morrison, Jeffrey A. Borgia, Michael J. Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. Mora Pinero, Mario Quintero-Aguilo, Carlos Gilberto Carlotti, Jose Sebastião Dos Santos, Rafael Kemp, Ajith Sankarankuty, Daniela Tirapelli, James Catto, Kathy Agnew, Elizabeth Swisher, Jenette Creaney, Bruce Robinson, Carl Simon Shelley, Eryn M. Godwin, Sara Kendall, Cassaundra Shipman, Carol Bradford, Thomas Carey, Andrea Haddad, Jeffey Moyer, Lisa Peterson, Mark Prince, Laura Rozek, Gregory Wolf, Rayleen Bowman, Kwun M. Fong, Ian Yang, Robert Korst, W. Kimryn Rathmell, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, John DiPersio, Bettina Drake, Ramaswamy Govindan, Sharon Heath, Timothy Ley, Brian Van Tine, Peter Westervelt, Mark A. Rubin, Jung Il Lee, Natália D. 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H., Bernard B., Chambwe N., Knijnenburg T., Kramer R., Leinonen K., Miller M., Reynolds S., Shmulevich I., Zhang W., Akbani R., Broom B.M., Hegde A.M., Ju Z., Kanchi R.S., Korkut A., Li J., Liang H., Ling S., Liu W., Lu Y., Mills G.B., Ng K.-S., Ryan M., Wang J., Zhang J., Abeshouse A., Armenia J., Chakravarty D., Chatila W.K., de Bruijn I., Gao J., Gross B.E., Heins Z.J., Kundra R., La K., Ladanyi M., Luna A., Nissan M.G., Ochoa A., Phillips S.M., Reznik E., Sanchez-Vega F., Sander C., Schultz N., Sheridan R., Sumer S.O., Sun Y., Taylor B.S., Anur P., Peto M., Spellman P., Benz C., Stuart J.M., Wong C.K., Yau C., Hayes D.N., Wilkerson M.D., Ally A., Balasundaram M., Brooks D., Carlsen R., Chuah E., Dhalla N., Jones S.J.M., Kasaian K., Lee D., Ma Y., Marra M.A., Mayo M., Moore R.A., Mungall A.J., Mungall K., Robertson A.G., Sadeghi S., Schein J.E., Sipahimalani P., Tam A., Thiessen N., Tse K., Wong T., Berger A.C., Beroukhim R., Cibulskis C., Gabriel S.B., Ha G., Meyerson M., Schumacher S.E., Shih J., Kucherlapati M.H., Kucherlapati R.S., Baylin S., Cope L., Danilova L., Bootwalla M.S., Lai P.H., Maglinte D.T., Van Den Berg D.J., Weisenberger D.J., Auman J.T., Balu S., Bodenheimer T., Fan C., Hoadley K.A., Hoyle A.P., Jefferys S.R., Jones C.D., Meng S., Mieczkowski P.A., Perou A.H., Perou C.M., Roach J., Shi Y., Simons J.V., Skelly T., Soloway M.G., Tan D., Veluvolu U., Fan H., Hinoue T., Laird P.W., Bellair M., Chang K., Covington K., Creighton C.J., Dinh H., Doddapaneni H., Donehower L.A., Drummond J., Gibbs R.A., Glenn R., Hale W., Han Y., Hu J., Korchina V., Lee S., Lewis L., Li W., Liu X., Morgan M., Morton D., Muzny D., Santibanez J., Sheth M., Shinbrot E., Wang L., Wang M., Wheeler D.A., Xi L., Zhao F., Hess J., Appelbaum E.L., Bailey M., Cordes M.G., Ding L., Fronick C.C., Fulton L.A., Fulton R.S., Kandoth C., Mardis E.R., McLellan M.D., Miller C.A., Schmidt H.K., Wilson R.K., Crain D., Curley E., Gardner J., Lau K., Mallery D., Morris S., Paulauskis J., Penny R., Shelton C., Shelton T., Sherman M., Thompson E., Yena P., Bowen J., Gastier-Foster J.M., Gerken M., Leraas K.M., Lichtenberg T.M., Ramirez N.C., Wise L., Zmuda E., Corcoran N., Costello T., Hovens C., Carvalho A.L., de Carvalho A.C., Fregnani J.H., Longatto-Filho A., Reis R.M., Scapulatempo-Neto C., Silveira H.C.S., Vidal D.O., Burnette A., Eschbacher J., Hermes B., Noss A., Singh R., Anderson M.L., Castro P.D., Ittmann M., Huntsman D., Kohl B., Le X., Thorp R., Andry C., Duffy E.R., Lyadov V., Paklina O., Setdikova G., Shabunin A., Tavobilov M., McPherson C., Warnick R., Berkowitz R., Cramer D., Feltmate C., Horowitz N., Kibel A., Muto M., Raut C.P., Malykh A., Barnholtz-Sloan J.S., Barrett W., Devine K., Fulop J., Ostrom Q.T., Shimmel K., Wolinsky Y., Sloan A.E., De Rose A., Giuliante F., Goodman M., Karlan B.Y., Hagedorn C.H., Eckman J., Harr J., Myers J., Tucker K., Zach L.A., Deyarmin B., Kvecher L., Larson C., Mural R.J., Somiari S., Vicha A., Zelinka T., Bennett J., Iacocca M., Rabeno B., Swanson P., Latour M., Lacombe L., Tetu B., Bergeron A., McGraw M., Staugaitis S.M., Chabot J., Hibshoosh H., Sepulveda A., Su T., Wang T., Potapova O., Voronina O., Desjardins L., Mariani O., Roman-Roman S., Sastre X., Stern M.-H., Cheng F., Signoretti S., Berchuck A., Bigner D., Lipp E., Marks J., McCall S., McLendon R., Secord A., Sharp A., Behera M., Brat D.J., Chen A., Delman K., Force S., Khuri F., Magliocca K., Maithel S., Olson J.J., Owonikoko T., Pickens A., Ramalingam S., Shin D.M., Sica G., Van Meir E.G., Eijckenboom W., Gillis A., Korpershoek E., Looijenga L., Oosterhuis W., Stoop H., van Kessel K.E., Zwarthoff E.C., Calatozzolo C., Cuppini L., Cuzzubbo S., DiMeco F., Finocchiaro G., Mattei L., Perin A., Pollo B., Chen C., Houck J., Lohavanichbutr P., Hartmann A., Stoehr C., Stoehr R., Taubert H., Wach S., Wullich B., Kycler W., Murawa D., Wiznerowicz M., Chung K., Edenfield W.J., Martin J., Baudin E., Bubley G., Bueno R., De Rienzo A., Richards W.G., Kalkanis S., Mikkelsen T., Scarpace L., Girard N., Aymerich M., Campo E., Gine E., Guillermo A.L., Van Bang N., Hanh P.T., Phu B.D., Tang Y., Colman H., Evason K., Dottino P.R., Martignetti J.A., Gabra H., Juhl H., Akeredolu T., Stepa S., Hoon D., Ahn K., Kang K.J., Beuschlein F., Breggia A., Birrer M., Bell D., Borad M., Bryce A.H., Castle E., Chandan V., Cheville J., Copland J.A., Farnell M., Flotte T., Giama N., Ho T., Kendrick M., Kocher J.-P., Kopp K., Moser C., Nagorney D., O'Brien D., O'Neill B.P., Patel T., Petersen G., Que F., Rivera M., Roberts L., Smallridge R., Smyrk T., Stanton M., Thompson R.H., Torbenson M., Yang J.D., Zhang L., Brimo F., Ajani J.A., Gonzalez A.M.A., Behrens C., Bondaruk J., Broaddus R., Czerniak B., Esmaeli B., Fujimoto J., Gershenwald J., Guo C., Lazar A.J., Logothetis C., Meric-Bernstam F., Moran C., Ramondetta L., Rice D., Sood A., Tamboli P., Thompson T., Troncoso P., Tsao A., Wistuba I., Carter C., Haydu L., Hersey P., Jakrot V., 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Kovatich A.J., Shriver C.D., DiPersio J., Drake B., Govindan R., Heath S., Ley T., Van Tine B., Westervelt P., Rubin M.A., Lee J.I., Aredes N.D., Mariamidze A., Serody J.S., Demicco E.G., Disis M.L., Vincent B.G., Shmulevich L., SAIC-F-Frederick, Inc, and Leidos Biomedical Research, Inc.
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Neuroblastoma RAS viral oncogene homolog ,Male ,0301 basic medicine ,INFORMATION ,PREDICTION ,Macrophage ,medicine.medical_treatment ,Lymphocyte ,Cell ,Cancer Genome Atlas Research Network ,COMPREHENSIVE ANALYSIS ,computer.software_genre ,GENOMIC ANALYSES ,0302 clinical medicine ,Transforming Growth Factor beta ,Neoplasms ,Immunologie ,LS2_1 ,immune subtypes ,LS4_6 ,Immunology and Allergy ,tumor immunology ,610 Medicine & health ,Child ,Th1-Th2 Balance ,immunomodulatory ,Aged, 80 and over ,T-CELL-RECEPTOR ,integrative network analysi ,cancer genomic ,Genomics ,Middle Aged ,Prognosis ,medicine.anatomical_structure ,cancer genomics ,immuno-oncology ,immunotherapy ,integrative network analysis ,tumor microenvironment ,Infectious Diseases ,1107 Immunology ,030220 oncology & carcinogenesis ,immune subtype ,Female ,GENÔMICA ,Life Sciences & Biomedicine ,Natural language processing ,Sentence ,Human ,Adult ,SEQUENCING DATA ,Adolescent ,Prognosi ,Immunology ,Cancer immunity ,Biology ,CLASSIFICATION ,Article ,NO ,Set (abstract data type) ,Interferon-gamma ,Young Adult ,03 medical and health sciences ,Immune system ,microRNA ,REVEALS ,medicine ,Humans ,Epigenetics ,Aged ,Tumor microenvironment ,Wound Healing ,Science & Technology ,business.industry ,REGULATORY NETWORK ,Macrophages ,Gene sets ,Scoring methods ,Immunotherapy ,SOMATIC MUTATIONS ,R package ,030104 developmental biology ,Cancer research ,Genomic ,Artificial intelligence ,business ,computer - Abstract
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across cancer types, we identified six immune subtypes—wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant—characterized by differences in macrophage or lymphocyte signatures, Th1:Th2 cell ratio, extent of intratumoral heterogeneity, aneuploidy, extent of neoantigen load, overall cell proliferation, expression of immunomodulatory genes, and prognosis. Specific driver mutations correlated with lower (CTNNB1, NRAS, or IDH1) or higher (BRAF, TP53, or CASP8) leukocyte levels across all cancers. Multiple control modalities of the intracellular and extracellular networks (transcription, microRNAs, copy number, and epigenetic processes) were involved in tumor-immune cell interactions, both across and within immune subtypes. Our immunogenomics pipeline to characterize these heterogeneous tumors and the resulting data are intended to serve as a resource for future targeted studies to further advance the field. Thorsson et al. present immunogenomics analyses of more than 10,000 tumors, identifying six immune subtypes that encompass multiple cancer types and are hypothesized to define immune response patterns impacting prognosis. This work provides a resource for understanding tumor-immune interactions, with implications for identifying ways to advance research on immunotherapy., 0, info:eu-repo/semantics/published
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- 2019
29. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
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Tathiane M. Malta, Artem Sokolov, Andrew J. Gentles, Tomasz Burzykowski, Laila Poisson, John N. Weinstein, Bożena Kamińska, Joerg Huelsken, Larsson Omberg, Olivier Gevaert, Antonio Colaprico, Patrycja Czerwińska, Sylwia Mazurek, Lopa Mishra, Holger Heyn, Alex Krasnitz, Andrew K. Godwin, Alexander J. Lazar, Joshua M. Stuart, Katherine A. Hoadley, Peter W. Laird, Houtan Noushmehr, Maciej Wiznerowicz, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, Gad Getz, David I. Heiman, Jaegil Kim, Michael S. Lawrence, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Han Liang, Shiyun Ling, Wenbin Liu, Yiling Lu, Gordon B. Mills, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Jianjiong Gao, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. 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Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. 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Jones C.D., Meng S., Mieczkowski P.A., Mose L.E., Perou A.H., Perou C.M., Roach J., Shi Y., Simons J.V., Skelly T., Soloway M.G., Tan D., Veluvolu U., Fan H., Hinoue T., Laird P.W., Shen H., Zhou W., Bellair M., Chang K., Covington K., Creighton C.J., Dinh H., Doddapaneni H., Donehower L.A., Drummond J., Gibbs R.A., Glenn R., Hale W., Han Y., Hu J., Korchina V., Lee S., Lewis L., Li W., Liu X., Morgan M., Morton D., Muzny D., Santibanez J., Sheth M., Shinbrot E., Wang L., Wang M., Wheeler D.A., Xi L., Zhao F., Hess J., Appelbaum E.L., Bailey M., Cordes M.G., Ding L., Fronick C.C., Fulton L.A., Fulton R.S., Kandoth C., Mardis E.R., McLellan M.D., Miller C.A., Schmidt H.K., Wilson R.K., Crain D., Curley E., Gardner J., Lau K., Mallery D., Morris S., Paulauskis J., Penny R., Shelton C., Shelton T., Sherman M., Thompson E., Yena P., Bowen J., Gastier-Foster J.M., Gerken M., Leraas K.M., Lichtenberg T.M., Ramirez N.C., Wise L., Zmuda E., Corcoran N., Costello T., Hovens C., Carvalho A.L., 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- Subjects
0301 basic medicine ,Carcinogenesis ,pan-cancer ,Cancer Genome Atlas Research Network ,medicine.disease_cause ,Biochemistry ,epigenomic ,Epigenesis, Genetic ,genomic ,Machine Learning ,GENE-EXPRESSION SIGNATURE ,TUMOR ,Neoplasms ,Databases, Genetic ,Tumor Microenvironment ,LS4_6 ,Stemness ,Neoplasm Metastasis ,610 Medicine & health ,Induced pluripotent stem cell ,11 Medical and Health Sciences ,Carcinogenesi ,Epigenomics ,Cancer stem cells ,Stem Cells ,PROLIFERATION ,MicroRNA ,Sciences bio-médicales et agricoles ,CANCER ,stemne ,Neoplasm Metastasi ,CONNECTIVITY MAP ,ALGORITMOS ,Stem cell ,Life Sciences & Biomedicine ,Human ,Biochemistry & Molecular Biology ,cancer stem cell ,The Cancer Genome Atlas ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,NO ,ANNEXIN 1 ,03 medical and health sciences ,Stem Cell ,Cancer stem cell ,medicine ,Humans ,Epigenetics ,EMBRYONIC STEM ,Tumor microenvironment ,Science & Technology ,Biochemistry, Genetics and Molecular Biology(all) ,dedifferentiation ,Cell Biology ,06 Biological Sciences ,Cell Dedifferentiation ,DNA Methylation ,Immune checkpoint ,SELF-RENEWAL ,MicroRNAs ,030104 developmental biology ,CELLS ,Cancer research ,Neoplasm ,OVEREXPRESSION ,The Cancer Genome Atla ,Transcriptome ,cancer stem cells ,machine learning ,stemness ,Genetics and Molecular Biology(all) ,Developmental Biology - Abstract
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation. Stemness features extracted from transcriptomic and epigenetic data from TCGA tumors reveal novel biological and clinical insight, as well as potential drug targets for anti-cancer therapies., 0, info:eu-repo/semantics/published
- Published
- 2018
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