Analysis of time-course gene expression profiles to study regulation of cell growth in fed-batch bioreactors

Biochemical Engineering Journal - Tập 103 - Trang 77-84 - 2015
Yanzhu Lin1, Kim Lehmann1, Philip Z. Brohawn1, Zheng Liu1, Nitin Agarwal1
1MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA

Tài liệu tham khảo

Matasci, 2008, Recombinant therapeutic protein production in cultivated mammalian cells: current status and future prospects, Drug Discov. Today: Technol., 5, e37, 10.1016/j.ddtec.2008.12.003 Zhu, 2012, Mammalian cell protein expression for biopharmaceutical production, Biotechnol. Adv., 30, 1158, 10.1016/j.biotechadv.2011.08.022 Walsh, 2010, Biopharmaceutical benchmarks 2010, Nat. Biotechnol., 28, 917, 10.1038/nbt0910-917 Wurm, 2004, Production of recombinant protein therapeutics in cultivated mammalian cells, Nat. Biotechnol., 22, 1393, 10.1038/nbt1026 Birch, 2006, Antibody production, Adv. Drug Deliv. Rev., 58, 671, 10.1016/j.addr.2005.12.006 Hacker, 2009, 25 years of recombinant proteins from reactor-grown cells—where do we go from here?, Biotechnol. Adv., 27, 1023, 10.1016/j.biotechadv.2009.05.008 Shukla, 2010, Recent advances in large-scale production of monoclonal antibodies and related proteins, Trends Biotechnol., 28, 253, 10.1016/j.tibtech.2010.02.001 Wuest, 2012, Genomics in mammalian cell culture bioprocessing, Biotechnol. Adv., 30, 629, 10.1016/j.biotechadv.2011.10.010 Castro-Melchor, 2012, Transcriptome data analysis for cell culture processes, 27 Stoughton, 2005, Applications of DNA microarrays in biology, Annu. Rev. Biochem., 74, 53, 10.1146/annurev.biochem.74.082803.133212 Sebastiani, 2003, Statistical challenges in functional genomics, Stat. Sci., 33 Hastie, 2004, Efficient quadratic regularization for expression arrays, Biostatistics, 5, 329, 10.1093/biostatistics/kxh010 Chun, 2010, Sparse partial least squares regression for simultaneous dimension reduction and variable selection, J. R. Stat. Soc.: Ser. B (Stat. Methodol.), 72, 3, 10.1111/j.1467-9868.2009.00723.x Boulesteix, 2007, Partial least squares: a versatile tool for the analysis of high-dimensional genomic data, Brief. Bioinform., 8, 32, 10.1093/bib/bbl016 Zhang, 2009, Penalized orthogonal-components regression for large p small n data, Electron. J. Stat., 3, 781, 10.1214/09-EJS354 Tibshirani, 1996, Regression shrinkage and selection via the lasso, J. R. Stat. Soc.: Ser. B (Methodol.), 58, 267 Zou, 2006, Sparse principal component analysis, J. Comput. Graph. Stat., 15, 265, 10.1198/106186006X113430 Alter, 2000, Singular value decomposition for genome-wide expression data processing and modeling, Proc. Natl. Acad. Sci., 97, 10101, 10.1073/pnas.97.18.10101 Johnson, 2007, Adjusting batch effects in microarray expression data using empirical Bayes methods, Biostatistics, 8, 118, 10.1093/biostatistics/kxj037 Leek, 2010, Tackling the widespread and critical impact of batch effects in high-throughput data, Nat. Rev. Genet., 11, 733, 10.1038/nrg2825 Imbeaud, 2005, Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces, Nucleic Acids Res., 33, e56, 10.1093/nar/gni054 Irizarry, 2003, Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics, 4, 249, 10.1093/biostatistics/4.2.249 Irizarry, 2002, Summaries of affymetrix GeneChip probe level data, Nucleic Acids Res., 31, e15, 10.1093/nar/gng015 Bolstad, 2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19, 185, 10.1093/bioinformatics/19.2.185 Gautier, 2004, Affy—analysis of affymetrix GeneChip data at the probe level, Bioinformatics., 20, 307, 10.1093/bioinformatics/btg405 Quackenbush, 2002, Microarray data normalization and transformation, Nat. Genet., 32, 496, 10.1038/ng1032 Schaub, 2010, CHO gene expression profiling in biopharmaceutical process analysis and design, Biotechnol. Bioeng., 105, 431, 10.1002/bit.22549 Charaniya, 2009, Mining transcriptome data for function–trait relationship of hyper productivity of recombinant antibody, Biotechnol. Bioeng., 102, 1654, 10.1002/bit.22210 Price, 2006, Principal components analysis corrects for stratification in genome-wide association studies, Nat. Genet., 38, 904, 10.1038/ng1847 Krämer, 2013, Causal analysis approaches in ingenuity pathway analysis (IPA), Bioinformatics, 30, 523, 10.1093/bioinformatics/btt703 Lutsenko, 2010, Human copper homeostasis: a network of interconnected pathways, Curr. Opin. Chem. Biol., 14, 211, 10.1016/j.cbpa.2010.01.003 van den, 2010, Posttranslational regulation of copper transporters, JBIC J. Biol. Inorg. Chem., 15, 37, 10.1007/s00775-009-0592-7 Huster, 2007, High copper selectively alters lipid metabolism and cell cycle machinery in the mouse model of Wilson disease, J. Biol. Chem., 282, 8343, 10.1074/jbc.M607496200 Huster, 2007, Wilson disease: not just a copper disorder. Analysis of a Wilson disease model demonstrates the link between copper and lipid metabolism, Mol. Biosyst., 3, 816, 10.1039/b711118p Ralle, 2010, Wilson disease at a single cell level: intracellular copper trafficking activates compartment-specific responses in hepatocytes, J. Biol. Chem., 285, 30875, 10.1074/jbc.M110.114447 Itoh, 2008, Novel role of antioxidant-1 (Atox1) as a copper-dependent transcription factor involved in cell proliferation, J. Biol. Chem., 283, 9157, 10.1074/jbc.M709463200 Rawson, 2003, The SREBP pathway—insights from Insigs and insects, Nat. Rev. Mol. Cell Biol., 4, 631, 10.1038/nrm1174 Sato, 2010, Sterol metabolism and SREBP activation, Arch. Biochem. Biophys., 501, 177, 10.1016/j.abb.2010.06.004 Owen, 2012, Insulin stimulation of SREBP-1c processing in transgenic rat hepatocytes requires p70 S6-kinase, Proc. Natl. Acad. Sci., 109, 16184, 10.1073/pnas.1213343109 Sengupta, 2010, Regulation of the mTOR complex 1 pathway by nutrients, growth factors, and stress, Mol. Cell, 40, 310, 10.1016/j.molcel.2010.09.026 Dodd, 2012, Leucine and mTORC1: a complex relationship, Am. J. Physiol.–Endocrinol. Metabol., 302, E1329, 10.1152/ajpendo.00525.2011 Tai, 2006, A multivariate empirical Bayes statistic for replicated microarray time course data, Ann. Stat., 34, 2387, 10.1214/009053606000000759