Development of a Drug-Response Modeling Framework to Identify Cell Line Derived Translational Biomarkers That Can Predict Treatment Outcome to Erlotinib or Sorafenib
作者： Bin Li , Hyunjin Shin , Georgy Gulbekyan , Olga Pustovalova , Yuri Nikolsky
DOI: 10.1371/JOURNAL.PONE.0130700
关键词: Gene regulatory network 、 Medicine 、 Erlotinib Hydrochloride 、 Clinical study design 、 Drug 、 Clinical trial 、 Sorafenib 、 Computational biology 、 Erlotinib 、 Bioinformatics 、 Drug discovery 、 General Biochemistry, Genetics and Molecular Biology 、 General Agricultural and Biological Sciences 、 General Medicine
摘要: Development of drug responsive biomarkers from pre-clinical data is a critical step in discovery, as it enables patient stratification clinical trial design. Such translational can be validated early phases and utilized inclusion parameter later stage trials. Here we present study on building accurate selective sensitivity models for Erlotinib or Sorafenib vitro data, followed by validation individual corresponding treatment arms generated the BATTLE trial. A Partial Least Squares Regression (PLSR) based modeling framework was designed implemented, using special splitting strategy canonical pathways to capture robust information model building. predictive could used identify sub-group patients that respond better treatment, these are specific drugs. The derived signature genes reflect each drug’s known mechanism action. Also, predict potential cancer indications consistent with results selection globally normalized GEO expression datasets.
harvard.edu
rti.org
paperity.org
core.ac.uk 参考文章(50)
Yuri Nikolsky, Eugene Kirillov, Roman Zuev, Eugene Rakhmatulin, Tatiana Nikolskaya, Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated “Knowledge-Based” Platform Methods in Molecular Biology. ,vol. 563, pp. 177- 196 ,(2009) , 10.1007/978-1-60761-175-2_10
Scudiero Da, Paull Kd, Abbott Bj, Shoemaker Rh, Monks A, Mayo Jg, Alley Mc, McLemore Tl, Boyd Mr, Fine Dl, Development of human tumor cell line panels for use in disease-oriented drug screening. Progress in Clinical and Biological Research. ,vol. 276, pp. 265- ,(1988)
Daniel Yekutieli, Yoav Benjamini, THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY Annals of Statistics. ,vol. 29, pp. 1165- 1188 ,(2001) , 10.1214/AOS/1013699998
Marina Bessarabova, Alexander Ishkin, Lellean JeBailey, Tatiana Nikolskaya, Yuri Nikolsky, Knowledge-based analysis of proteomics data BMC Bioinformatics. ,vol. 13, pp. 1- 19 ,(2012) , 10.1186/1471-2105-13-S16-S13
Edward S Kim, Roy S Herbst, Ignacio I Wistuba, J Jack Lee, George R Blumenschein Jr, Anne Tsao, David J Stewart, Marshall E Hicks, Jeremy Erasmus Jr, Sanjay Gupta, Christine M Alden, Suyu Liu, Ximing Tang, Fadlo R Khuri, Hai T Tran, Bruce E Johnson, John V Heymach, Li Mao, Frank Fossella, Merrill S Kies, Vassiliki Papadimitrakopoulou, Suzanne E Davis, Scott M Lippman, Waun K Hong, None, The BATTLE Trial: Personalizing Therapy for Lung Cancer Cancer Discovery. ,vol. 1, pp. 44- 53 ,(2011) , 10.1158/2159-8274.CD-10-0010
Kim-Anh Lê Cao, Simon Boitard, Philippe Besse, Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems BMC Bioinformatics. ,vol. 12, pp. 253- 253 ,(2011) , 10.1186/1471-2105-12-253
Daniela M Witten, Robert J. Tibshirani, Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data Statistical Applications in Genetics and Molecular Biology. ,vol. 8, pp. 1- 27 ,(2009) , 10.2202/1544-6115.1470
C. Virtanen, Y. Ishikawa, D. Honjoh, M. Kimura, M. Shimane, T. Miyoshi, H. Nomura, M. H. Jones, Integrated classification of lung tumors and cell lines by expression profiling Proceedings of the National Academy of Sciences of the United States of America. ,vol. 99, pp. 12357- 12362 ,(2002) , 10.1073/PNAS.192240599
Fenghuang Zhan, Bart Barlogie, George Mulligan, John D. Shaughnessy, Barb Bryant, High-risk myeloma: a gene expression based risk-stratification model for newly diagnosed multiple myeloma treated with high-dose therapy is predictive of outcome in relapsed disease treated with single-agent bortezomib or high-dose dexamethasone Blood. ,vol. 111, pp. 968- 969 ,(2008) , 10.1182/BLOOD-2007-10-119321
Leming Shi, Gregory Campbell, Wendell D Jones, Fabien Campagne, Zhining Wen, Stephen J Walker, Zhenqiang Su, Tzu-Ming Chu, Federico M Goodsaid, Lajos Pusztai, JD Shaughnessy Jr, Andr? Oberthuer, Russell S Thomas, Richard S Paules, Mark Fielden, Bart Barlogie, Weijie Chen, Pan Du, Matthias Fischer, Cesare Furlanello, Brandon D Gallas, Xijin Ge, Dalila B Megherbi, W Fraser Symmans, May D Wang, John Zhang, Hans Bitter, Benedikt Brors, Pierre R Bushel, Max Bylesjo, Minjun Chen, Jie Cheng, J Chou, TS Davison, M Delorenzi, Y Deng, V Devanarayan, DJ Dix, J Dopazo, KC Dorff, F Elloumi, J Fan, S Fan, X Fan, H Fang, N Gonzaludo, KR Hess, H Hong, J Huan, RA Irizarry, R Judson, D Juraeva, S Lababidi, CG Lambert, L Li, Y Li, Z Li, SM Lin, G Liu, EK Lobenhofer, J Luo, W Luo, MN McCall, Y Nikolsky, GA Pennello, RG Perkins, R Philip, V Popovici, ND Price, F Qian, A Scherer, T Shi, W Shi, J Sung, D Thierry-Mieg, J Thierry-Mieg, V Thodima, J Trygg, L Vishnuvajjala, SJ Wang, J Wu, Y Wu, Q Xie, WA Yousef, L Zhang, X Zhang, S Zhong, Y Zhou, S Zhu, D Arasappan, W Bao, AB Lucas, F Berthold, RJ Brennan, A Buness, JG Catalano, C Chang, R Chen, Y Cheng, J Cui, W Czika, F Demichelis, X Deng, D Dosymbekov, R Eils, Y Feng, J Fostel, S Fulmer-Smentek, JC Fuscoe, L Gatto, W Ge, DR Goldstein, L Guo, DN Halbert, J Han, SC Harris, C Hatzis, D Herman, J Huang, RV Jensen, R Jiang, CD Johnson, G Jurman, Y Kahlert, SA Khuder, M Kohl, J Li, M Li, QZ Li, S Li, J Liu, Y Liu, Z Liu, L Meng, M Madera, F Martinez-Murillo, I Medina, J Meehan, K Miclaus, RA Moffitt, D Montaner, P Mukherjee, GJ Mulligan, P Neville, T Nikolskaya, B Ning, GP Page, J Parker, RM Parry, X Peng, The Microarray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models Nature Biotechnology. ,vol. 28, pp. 827- 838 ,(2010) , 10.1038/NBT.1665