Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity

Journal of Biotechnology

Volumn 155, Issue 3, 2011, Pages 350-359

  Clarke, Colin ^a   Doolan, Padraig ^a   Barron, Niall ^a   Meleady, Paula ^a   O'Sullivan, Finbarr ^a   Gammell, Patrick ^b   Melville, Mark ^b   Leonard, Mark ^b   Clynes, Martin ^a  

^a DUBLIN CITY UNIVERSITY   (Ireland)

^b PFIZER INC   (United States)

Author keywords

Cell specific productivity; Chinese hamster ovary; Coexpression analysis; Gene expression; Growth rate; Microarray

Indexed keywords

BIOLOGICAL PROCESS; BIOPROCESSES; CELL CYCLE; CELL DENSITY; CELL LINES; CELL-SPECIFIC PRODUCTIVITY; CHINESE HAMSTER OVARY; CHINESE HAMSTER OVARY CELLS; CHO CELL; CO-EXPRESSION; CO-EXPRESSION NETWORKS; COEXPRESSED GENES; CULTURE GROWTH; DATA SETS; FUSION PROTEINS; GENE EXPRESSION ANALYSIS; PRODUCT TYPES; PROTEIN SECRETION; SEEDING DENSITY; SPECIFIC PRODUCTIVITY; TRANSCRIPTIONAL MODULES; TRANSCRIPTOMES; VESICLE TRANSPORT;

AMMONIUM COMPOUNDS; CELLS; ELECTRIC NETWORK ANALYSIS; GENE EXPRESSION; GROWTH RATE; MICROARRAYS; MONOCLONAL ANTIBODIES; PRODUCTIVITY; SCALES (WEIGHING INSTRUMENTS);

CELL CULTURE;

AMMONIA; BIOLOGICAL FACTOR; HYBRID PROTEIN; LACTIC ACID; MONOCLONAL ANTIBODY; TRANSCRIPTOME;

AMMONIA FORMATION; ANIMAL CELL; ARTICLE; BIOPROCESS; CELL CULTURE; CELL CYCLE; CELL DENSITY; CELL GROWTH; CELL LINE; CELL SPECIFICITY; CELL TRANSPORT; CELL VACUOLE; CELL VIABILITY; CHO CELL; CULTURE MEDIUM; FEMALE; GENE CLUSTER; GENE EXPRESSION SYSTEM; GENE IDENTIFICATION; MICROARRAY ANALYSIS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN SECRETION; TEMPERATURE;

ANIMALS; CELL LINE; CHO CELLS; CRICETINAE; CRICETULUS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOME; RECOMBINANT PROTEINS; RNA, MESSENGER; SOFTWARE; SYSTEMS BIOLOGY;

CRICETULUS GRISEUS;

EID: 80052389765     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2011.07.011     Document Type: Article

References (58)

1. Anelli T., Alessio M., Mezghrani A., Simmen T., Talamo F., Bachi A., Sitia R. ERp44, a novel endoplasmic reticulum folding assistant of the thioredoxin family. EMBO J. 2002, 21:835-844.
2. Aoyama T., Wakui K., Orii K.E., Hashimoto T., Fukushima Y. Fluorescence in situ hybridization mapping of the alpha and beta subunits (HADHA and HADHB) of human mitochondrial fatty acid beta-oxidation multienzyme complex to 2p23 and their evolution. Cytogenet. Cell Genet. 1997, 79:221-224.
3. Baik J.Y., Lee M.S., An S.R., Yoon S.K., Joo E.J., Kim Y.H., Park H.W., Lee G.M. Initial transcriptome and proteome analyses of low culture temperature-induced expression in CHO cells producing erythropoietin. Biotechnol. Bioeng. 2006, 93:361-371.
4. Blum R., Feick P., Puype M., Vandekerckhove J., Klengel R., Nastainczyk W., Schulz I. Tmp21 and p24A, two type I proteins enriched in pancreatic microsomal membranes, are members of a protein family involved in vesicular trafficking. J. Biol. Chem. 1996, 271:17183-17189.
5. Borman L.S., Branda R.F. Nutritional folate-deficiency in Chinese-hamster ovary cells. 1. Characterization of the pleiotropic response and its modulation by nucleic-acid precursors. J. Cell. Physiol. 1989, 140:335-343.
6. 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. J. Biotechnol. 2011, 151:159-165.
7. Coleman R.A., Lewin T.M., Van Horn C.G., Gonzalez-Baro M.R. Do long-chain acyl-CoA synthetases regulate fatty acid entry into synthetic versus degradative pathways?. J. Nutr. 2002, 132:2123-2126.
8. Dahms T.E.S., Sainz G., Giroux E.L., Caperelli C.A., Smith J.L. The Apo and ternary complex structures of a chemotherapeutic target: human glycinamide ribonucleotide transformylase. Biochemistry 2005, 44:9841-9850.
9. Di Pietro E., Wang X.L., MacKenzie R.E. The expression of mitochondrial methylenetetrahydrofolate dehydrogenase-cyclohydrolase supports a role in rapid cell growth. Biochim. Biophys. Acta, Gen. Subj. 2004, 1674:78-84.
10. 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. Biotechnol. Bioeng. 2010, 106:42-56.
11. Doolan P., Melville M., Gammell P., Sinacore M., Meleady P., McCarthy K., Francullo L., Leonard M., Charlebois T., Clynes M. Transcriptional profiling of gene expression changes in a PACE-transfected CHO DUKX cell line secreting high levels of rhBMP-2. Mol. Biotechnol. 2008, 39:187-199.
12. Edenberg H.J. Regulation of the mammalian alcohol dehydrogenase genes. Prog. Nucleic Acid Res. Mol. Biol. 2000, 64:295-341.
13. Forsburg S.L. Eukaryotic MCM proteins: beyond replication initiation. Microbiol. Mol. Biol. Rev. 2004, 68:109-131.
14. Fujita J. Cold shock response in mammalian cells. J. Mol. Microbiol. Biotechnol. 1999, 1:243-255.
15. Goldberg I.J., Merkel M. Lipoprotein lipase: physiology, biochemistry, and molecular biology. Front. Biosci. 2001, 6:D388-D405.
16. Griffin T.J., Seth G., Xie H.W., Bandhakavi S., Hu W.S. Advancing mammalian cell culture engineering using genome-scale technologies. Trends Biotechnol. 2007, 25:401-408.
17. Guo Y., Punj V., Sengupta D., Linstedt A.D. Coat-tether interaction in Golgi organization. Mol. Biol. Cell 2008, 19:2830-2843.
18. Gupta P., Lee K.H. Genomics and proteomics in process development: opportunities and challenges. Trends Biotechnol. 2007, 25:324-330.
19. Hogenboom S., Tuyp J.J., Espeel M., Koster J., Wanders R.J., Waterham H.R. Human mevalonate pyrophosphate decarboxylase is localized in the cytosol. Mol. Genet. Metab. 2004, 81:216-224.
20. Horvath S., Dong J. Geometric interpretation of gene coexpression network analysis. PLoS Comput. Biol. 2008, 4:e1000117.
21. Horvath S., Zhang B., Carlson M., Lu K.V., Zhu S., Felciano R.M., Laurance M.F., Zhao W., Qi S., Chen Z., Lee Y., Scheck A.C., Liau L.M., Wu H., Geschwind D.H., Febbo P.G., Kornblum H.I., Cloughesy T.F., Nelson S.F., Mischel P.S. Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:17402-17407.
22. Hu G., Cabrera A., Kono M., Mok S., Chaal B.K., Haase S., Engelberg K., Cheemadan S., Spielmann T., Preiser P.R., Gilberger T.W., Bozdech Z. Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat. Biotechnol. 2010, 28:91-98.
23. Hu T., Miller C.M., Ridder G.M., Aardema M.J. Characterization of p53 in Chinese hamster cell lines CHO-K1, CHO-WBL, and CHL: implications for genotoxicity testing. Mutat. Res., Fundam. Mol. Mech. Mutagen. 1999, 426:51-62.
24. Hwang Y.C., Lu T.Y., Huang D.Y., Kuo Y.S., Kao C.F., Yeh N.H., Wu H.C., Lin C.T. NOLC1, an enhancer of nasopharyngeal carcinoma progression, is essential for TP53 to regulate MDM2 expression. Am. J. Pathol. 2009, 175:342-354.
25. Jelsema C.L., Morre D.J. Distribution of phospholipid biosynthetic enzymes among cell components of rat liver. J. Biol. Chem. 1978, 253:7960-7971.
26. Kenmochi N., Kawaguchi T., Rozen S., Davis E., Goodman N., Hudson T.J., Tanaka T., Page D.C. A map of 75 human ribosomal protein genes. Genome Res. 1998, 8:509-523.
27. Kumar N., Gammell P., Clynes M. Proliferation control strategies to improve productivity and survival during CHO based production culture - a summary of recent methods employed and the effects of proliferation control in product secreting CHO cell lines. Cytotechnology 2007, 53:33-46.
28. Langfelder P., Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 2008, 9:599.
29. Lee I., Ambaru B., Thakkar P., Marcotte E.M., Rhee S.Y. Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol. 2010, 28:149-156.
30. Lippincott-Schwartz J., Liu W. Insights into COPI coat assembly and function in living cells. Trends Cell Biol. 2006, 16:e1-e4.
31. Maga G., Hubscher U. Proliferating cell nuclear antigen (PCNA): a dancer with many partners. J. Cell Sci. 2003, 116:3051-3060.
32. Martin D., Piulachs M.D., Cunillera N., Ferrer A., Belles X. Mitochondrial targeting of farnesyl diphosphate synthase is a widespread phenomenon in eukaryotes. Biochim. Biophys. Acta 2007, 1773:419-426.
33. Mason M.J., Fan G., Plath K., Zhou Q., Horvath S. Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics 2009, 10:327.
34. Mehrabian M., Callaway K.A., Clarke C.F., Tanaka R.D., Greenspan M., Lusis A.J., Sparkes R.S., Mohandas T., Edmond J., Fogelman A.M., et al. Regulation of rat liver 3-hydroxy-3-methylglutaryl coenzyme A synthase and the chromosomal localization of the human gene. J. Biol. Chem. 1986, 261:16249-16255.
35. Melville M., Doolan P., Mounts W., Barron N., Hann L., Leonard M., Clynes M., Charlebois T. Development and characterization of a Chinese hamster ovary cell-specific oligonucleotide microarray. Biotechnol. Lett. 2011.
36. Nikiforov M.A., Chandriani S., O'Connell B., Petrenko O., Kotenko I., Beavis A., Sedivy J.M., Cole M.D. A functional screen for Myc-responsive genes reveals serine hydroxymethyltransferase, a major source of the one-carbon unit for cell metabolism. Mol. Cell. Biol. 2002, 22:5793-5800.
37. Okuwaki M. The structure and functions of NPM1/Nucleophsmin/B23, a multifunctional nucleolar acidic protein. J. Biochem. 2008, 143:441-448.
38. Oldham M.C., Horvath S., Geschwind D.H. Conservation and evolution of gene colexpression networks in human and chimpanzee brains. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:17973-17978.
39. Ravasz E., Somera A.L., Mongru D.A., Oltvai Z.N., Barabasi A.L. Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555.
40. Rayl E.A., Moroson B.A., Beardsley G.P. The human purH gene product, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase IMP cyclohydrolase - cloning, sequencing, expression, purification, kinetic analysis, and domain mapping. J. Biol. Chem. 1996, 271:2225-2233.
41. Rudel L.L., Lee R.G., Parini P. ACAT2 is a target for treatment of coronary heart disease associated with hypercholesterolemia. Arterioscler. Thromb. Vasc. Biol. 2005, 25:1112-1118.
42. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13:2498-2504.
43. Sironi L., Mapelli M., Knapp S., De Antoni A., Jeang K.T., Musacchio A. Crystal structure of the tetrameric Mad1-Mad2 core complex: implications of 'safety belt' binding mechanism for the spindle checkpoint. EMBO J. 2002, 21:2496-2506.
44. Stuart J.M., Segal E., Koller D., Kim S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302:249-255.
45. 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. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:15545-15550.
46. Vainauskas S., Menon A.K. Endoplasmic reticulum localization of Gaa1 and PIG-T, subunits of the glycosylphosphatidylinositol transamidase complex. J. Biol. Chem. 2005, 280:16402-16409.
47. van Noort V., Snel B., Huynen M.A. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. EMBO Rep. 2004, 5:280-284.
48. Volchuk A., Sargeant R., Sumitani S., Liu Z., He L., Klip A. Cellubrevin is a resident protein of insulin-sensitive GLUT4 glucose transporter vesicles in 3T3-L1 adipocytes. J. Biol. Chem. 1995, 270:8233-8240.
49. Wolfe C.J., Kohane I.S., Butte A.J. Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinf. 2005, 6:227.
50. Wurm F.M. Production of recombinant protein therapeutics in cultivated mammalian cells. Nat. Biotechnol. 2004, 22:1393-1398.
51. Xu D., Joglekar A.P., Williams A.L., Hay J.C. Subunit structure of a mammalian ER/Golgi SNARE complex. J. Biol. Chem. 2000, 275:39631-39639.
52. Yee J.C., Gatti M.D., Philp R.J., Yap M., Hu W.S. Genomic and proteomic exploration of CHO and hybridoma cells under sodium butyrate treatment. Biotechnol. Bioeng. 2008, 99:1186-1204.
53. Yee J.C., Gerdtzen Z.P., Hu W.S. Comparative transcriptome analysis to unveil genes affecting recombinant protein productivity in mammalian cells. Biotechnol. Bioeng. 2009, 102:246-263.
54. Yoshida Y., Noshiro M., Aoyama Y., Kawamoto T., Horiuchi T., Gotoh O. Structural and evolutionary studies on sterol 14-demethylase P450 (CYP51), the most conserved P450 monooxygenase: II. Evolutionary analysis of protein and gene structures. J. Biochem. 1997, 122:1122-1128.
55. Yu H. Cdc20: a WD40 activator for a cell cycle degradation machine. Mol. Cell 2007, 27:3-16.
56. Yu H., Li M., Tint G.S., Chen J., Xu G., Patel S.B. Selective reconstitution of liver cholesterol biosynthesis promotes lung maturation but does not prevent neonatal lethality in Dhcr7 null mice. BMC Dev. Biol. 2007, 7:27.
57. Yudin D., Fainzilber M. Ran on tracks - cytoplasmic roles for a nuclear regulator. J. Cell Sci. 2009, 122:587-593.
58. Zhang B., Horvath S. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 2005, 4. Article17.