Transcriptomic analysis of clonal growth rate variation during CHO cell line development

Journal of Biotechnology

Volumn 166, Issue 3, 2013, Pages 105-113

  Doolan, Padraig ^a   Clarke, Colin ^a   Kinsella, Paula ^a   Breen, Laura ^a   Meleady, Paula ^a   Leonard, Mark ^b   Zhang, Lin ^b   Clynes, Martin ^a   Aherne, Sinead T ^a   Barron, Niall ^a  

^a DUBLIN CITY UNIVERSITY   (Ireland)

^b PFIZER INC   (United States)

Author keywords

Cell line development; Chinese hamster ovary; CHO; Growth rate; Microarray; MiRNA

Indexed keywords

CELL LINES; CELLULAR HOMEOSTASIS; CHINESE HAMSTER OVARY; CHINESE HAMSTER OVARY CELLS; CHO; DIFFERENTIAL EXPRESSIONS; GENE EXPRESSION ANALYSIS; MIRNA;

CELL CULTURE; GROWTH RATE; MICROARRAYS; POLYMERASE CHAIN REACTION; RNA;

GENE EXPRESSION;

MESSENGER RNA; MICRORNA; MICRORNA 17 19; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CELL CYCLE; CELL GROWTH; CELL LINE; CELL PROLIFERATION; COMPUTER MODEL; CONTROLLED STUDY; DOWN REGULATION; GENE; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GROWTH RATE; HOMEOSTASIS; MICROARRAY ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA TRANSLATION; TRANSCRIPTOMICS; UPREGULATION;

ANIMALS; CELL CYCLE; CELL PROLIFERATION; CELL SURVIVAL; CHO CELLS; CRICETINAE; CRICETULUS; DOWN-REGULATION; GENE EXPRESSION PROFILING; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; UP-REGULATION;

CRICETULUS GRISEUS;

EID: 84879212335     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2013.04.014     Document Type: Article

References (32)

1. Altamirano C., Paredes C., Cairo J.J., Godia F. Improvement of CHO cell culture medium formulation: simultaneous substitution of glucose and glutamine. Biotechnology Progress 2000, 16:69-75.
2. Barron N., Kumar N., Sanchez N., Doolan P., Clarke C., Meleady P., O'Sullivan F., Clynes M. Engineering CHO cell growth and recombinant protein productivity by overexpression of miR-7. Journal of Biotechnology 2011, 151:204-211.
3. Baycin-Hizal D., Tabb D.L., Chaerkady R., Chen L., Lewis N.E., Nagarajan H., Sarkaria V., Kumar A., Wolozny D., Colao J., Jacobson E., Tian Y., O'Meally R.N., Krag S.S., Cole R.N., Palsson B.O., Zhang H., Betenbaugh M. Proteomic analysis of Chinese hamster ovary cells. Journal of Proteome Research 2012, 11:5265-5276.
4. Birzele F., Schaub J., Rust W., Clemens C., Baum P., Kaufmann H., Weith A., Schulz T.W., Hildebrandt T. Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing. Nucleic Acids Research 2010, 38:3999-4010.
5. Bolstad B.M., Irizarry R.A., Astrand M., Speed T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
6. Brocker C., Lassen N., Estey T., Pappa A., Cantore M., Orlova V.V., Chavakis T., Kavanagh K.L., Oppermann U., Vasiliou V. Aldehyde dehydrogenase 7A1 (ALDH7A1) is a novel enzyme involved in cellular defense against hyperosmotic stress. Journal of Biological Chemistry 2010, 285:18452-18463.
7. Brocker C., Cantore M., Failli P., Vasiliou V. Aldehyde dehydrogenase 7A1 (ALDH7A1) attenuates reactive aldehyde and oxidative stress induced cytotoxicity. Chemico-Biological Interactions 2011, 191:269-277.
8. Burleigh S.C., van de Laar T., Stroop C.J., van Grunsven W.M., O'Donoghue N., Rudd P.M., Davey G.P. Synergizing metabolic flux analysis and nucleotide sugar metabolism to understand the control of glycosylation of recombinant protein in CHO cells. BMC Biotechnology 2011, 11:95.
9. Butler M. Animal cell cultures: recent achievements and perspectives in the production of biopharmaceuticals. Applied Microbiology and Biotechnology 2005, 68:283-291.
10. Clarke C., Doolan P., Barron N., Meleady P., O'Sullivan F., Gammell P., Melville M., Leonard M., Clynes M. Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity. Journal of Biotechnology 2011, 155:350-359.
11. Clarke C., Doolan P., Barron N., Meleady P., O'Sullivan F., Gammell P., Melville M., Leonard M., Clynes M. Predicting cell-specific productivity from CHO gene expression. Journal of Biotechnology 2011, 151:159-165.
12. Clarke C., Doolan P., Barron N., Meleady P., Madden S.F., Dinino D., Leonard M., Clynes M. CGCDB: a web-based resource for the investigation of gene coexpression in CHO cell culture. Biotechnology and Bioengineering 2012, 109:1368-1370.
13. Clarke C., Henry M., Doolan P., Kelly S., Aherne S., Sanchez N., Kelly P., Kinsella P., Breen L., Madden S.F., Zhang L., Leonard M., Clynes M., Meleady P., Barron N. Integrated miRNA, mRNA and protein expression analysis reveals the role of post-transcriptional regulation in controlling CHO cell growth rate. BMC Genomics 2012, 13:656.
14. Datta P., Linhardt R.J., Sharfstein S.T. An 'omics approach towards CHO cell engineering. Biotechnology and Bioengineering 2013, 110:1255-1271.
15. Doolan P., Meleady P., Barron N., Henry M., Gallagher R., Gammell P., Melville M., Sinacore M., McCarthy K., Leonard M., Charlebois T., Clynes M. Microarray and proteomics expression profiling identifies several candidates, including the valosin-containing protein (VCP), involved in regulating high cellular growth rate in production CHO cell lines. Biotechnology and Bioengineering 2010, 106:42-56.
16. Druz A., Son Y.J., Betenbaugh M., Shiloach J. Stable inhibition of mmu-miR-466h-5p improves apoptosis resistance and protein production in CHO cells. Metabolic Engineering 2013, 16C:87-94.
17. Gammell P., Barron N., Kumar N., Clynes M. Initial identification of low temperature and culture stage induction of miRNA expression in suspension CHO-K1 cells. Journal of Biotechnology 2007, 130:213-218.
18. Gonzalez-Leal I.J., Carrillo-Cocom L.M., Ramirez-Medrano A., Lopez-Pacheco F., Bulnes-Abundis D., Webb-Vargas Y., Alvarez M.M. Use of a Plackett-Burman statistical design to determine the effect of selected amino acids on monoclonal antibody production in CHO cells. Biotechnology Progress 2011, 27:1709-1717.
19. Hackl M., Jakobi T., Blom J., Doppmeier D., Brinkrolf K., Szczepanowski R., Bernhart S.H., Siederdissen C.H., Bort J.A., Wieser M., Kunert R., Jeffs S., Hofacker I.L., Goesmann A., Puhler A., Borth N., Grillari J. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology 2011, 153:62-75.
20. Hammond S., Kaplarevic M., Borth N., Betenbaugh M.J., Lee K.H. Chinese hamster genome database: an online resource for the CHO community at www.CHOgenome.org. Biotechnology and Bioengineering 2012, 109:1353-1356.
21. Hernandez Bort J.A., Hackl M., Hoflmayer H., Jadhav V., Harreither E., Kumar N., Ernst W., Grillari J., Borth N. Dynamic mRNA and miRNA profiling of CHO-K1 suspension cell cultures. Biotechnology Journal 2011, 7:500-515.
22. Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., Speed T.P. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research 2003, 31:e15.
23. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
24. Lewis B.P., Burge C.B., Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
25. Meleady P., Doolan P., Henry M., Barron N., Keenan J., O'Sullivan F., Clarke C., Gammell P., Melville M.W., Leonard M., Clynes M. Sustained productivity in recombinant Chinese hamster ovary (CHO) cell lines: proteome analysis of the molecular basis for a process-related phenotype. BMC Biotechnology 2011, 11:78.
26. Meleady P., Hoffrogge R., Henry M., Rupp O., Bort J.H., Clarke C., Brinkrolf K., Kelly S., Muller B., Doolan P., Hackl M., Beckmann T.F., Noll T., Grillari J., Barron N., Puhler A., Clynes M., Borth N. Utilization and evaluation of CHO-specific sequence databases for mass spectrometry based proteomics. Biotechnology and Bioengineering 2012, 109:1386-1394.
27. Prentice H.L., Ehrenfels B.N., Sisk W.P. Improving performance of mammalian cells in fed-batch processes through "bioreactor evolution". Biotechnology Progress 2007, 23:458-464.
28. Rozen S., Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 2000, 132:365-386.
29. Singh P.B. HP1 proteins - what is the essential interaction?. Genetika 2010, 46:1424-1429.
30. Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., Paulovich A., Pomeroy S.L., Golub T.R., Lander E.S., Mesirov J.P. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15545-15550.
31. Wurm F.M. Production of recombinant protein therapeutics in cultivated mammalian cells. Nature Biotechnology 2004, 22:1393-1398.
32. Yamaguchi Y., Ruoslahti E. Expression of human proteoglycan in Chinese hamster ovary cells inhibits cell proliferation. Nature 1988, 336:244-246.