Dynamic gene expression for metabolic engineering of mammalian cells in culture

Metabolic Engineering

Volumn 20, Issue , 2013, Pages 212-220

  Le, Huong ^a   Vishwanathan, Nandita ^a   Kantardjieff, Anne ^a   Doo, Inseok ^a   Srienc, Michael ^a   Zheng, Xiaolu ^a   Somia, Nikunj ^b   Hu, Wei Shou ^a  

^a University of Minnesota   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Fructose transporter (GLUT5); Lactate consumption; Promoter engineering; Thioredoxin interacting protein (Txnip); Time series transcriptome data

Indexed keywords

ANIMAL CELL CULTURE; DIGITAL STORAGE; FRUCTOSE; METABOLIC ENGINEERING; PRODUCTIVITY; RECOMBINANT PROTEINS;

CHINESE HAMSTER OVARY CELLS; CONSTITUTIVE EXPRESSIONS; LACTATE CONSUMPTION; PROCESS CHARACTERISTICS; THIOREDOXIN-INTERACTING PROTEIN (TXNIP); TIME-DEPENDENT EXPRESSION; TRANSCRIPTOME DATUM; TRANSGENE EXPRESSION;

GENE EXPRESSION;

LACTIC ACID; THIOREDOXIN INTERACTING PROTEIN;

ANIMAL CELL; ARTICLE; CELL CULTURE; CELL GROWTH; CHO CELL; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GROWTH RATE; MAMMAL CELL; METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTOMICS; TRANSGENE;

CRICETULUS GRISEUS; MAMMALIA;

FRUCTOSE TRANSPORTER (GLUT5); LACTATE CONSUMPTION; PROMOTER ENGINEERING; THIOREDOXIN-INTERACTING PROTEIN (TXNIP); TIME-SERIES TRANSCRIPTOME DATA;

ANIMALS; CHO CELLS; CRICETINAE; CRICETULUS; GENE EXPRESSION REGULATION; GLUCOSE TRANSPORT PROTEINS, FACILITATIVE; METABOLIC ENGINEERING; MICE; PROMOTER REGIONS, GENETIC;

EID: 84886993912     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2013.09.004     Document Type: Article

References (52)

1. Aggarwal S. What's fueling the biotech engine-2010 to 2011. Nature Biotechnology 2011, 29:1083-1089.
2. Alter O., Brown P.O., Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proceedings of the National Academy of Sciences 2000, 97:10101-10106.
3. Boch J., Scholze H., Schornack S., Landgraf A., Hahn S., Kay S., Lahaye T., Nickstadt A., Bonas U. Breaking the code of DNA binding specificity of Tal-type Iii effectors. Science 2009, 326:1509-1512.
4. 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.
5. Broad Institute, Mesocricetus Auratus Genome Sequencing., 2011. http://Www.Ncbi.Nlm.Nih.Gov/Bioproject?Term=77797%5bTop_Bioproject%5d%20and%20%22genome%20sequencing%22%5bProject%20data%20type%5d.
6. Carninci P., Sandelin A., Lenhard B., Katayama S., Shimokawa K., Ponjavic J., Semple C.A.M., Taylor M.S., Engström P.G., Frith M.C., Forrest A.R.R., Alkema W.B., Tan S.L., Plessy C., Kodzius R., Ravasi T., Kasukawa T., Fukuda S., Kanamori-Katayama M., Kitazume Y., Kawaji H., Kai C., Nakamura M., Konno H., Nakano K., Mottagui-Tabar S., Arner P., Chesi A., Gustincich S., Persichetti F., Suzuki H., Grimmond S.M., Wells C.A., Orlando V., Wahlestedt C., Liu E.T., Harbers M., Kawai J., Bajic V.B., Hume D.A., Hayashizaki Y. Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genetics 2006, 38:626-635.
7. Christian M., Cermak T., Doyle E.L., Schmidt C., Zhang F., Hummel A., Bogdanove A.J., Voytas D.F. Targeting DNA double-strand breaks with Tal effector nucleases. Genetics 2010, 186:757-761.
8. Cong L., Ran F.A., Cox D., Lin S., Barretto R., Habib N., Hsu P.D., Wu X., Jiang W., Marraffini L.A., Zhang F. Multiplex genome engineering using Crispr/Cas systems. Science 2013, 339:819-823.
9. Datta P., Linhardt R.J., Sharfstein S.T. An omics approach towards Cho cell engineering. Biotechnology and Bioengineering 2013, 110:1255-1271.
10. Doniger S., Salomonis N., Dahlquist K., Vranizan K., Lawlor S., Conklin B. Mappfinder: using gene ontology and genmapp to create a global gene-expression profile from microarray data. Genome Biology 2003, 4:R7.
11. Dorai H., Kyung Y.S., Ellis D., Kinney C., Lin C., Jan D., Moore G., Betenbaugh M.J. Expression of anti-apoptosis genes alters lactate metabolism of Chinese hamster ovary cells in culture. Biotechnology and Bioengineering 2009, 103:592-608.
12. Dorer D.R., Henikoff S. Expansions of transgene repeats cause heterochromatin formation and gene silencing in drosophila. Cell 1994, 77:993-1002.
13. Ernst W., Trummer E., Mead J., Bessant C., Strelec H., Katinger H., Hesse F. Evaluation of a genomics platform for cross-species transcriptome analysis of recombinant Cho cells. Biotechnology Journal 2006, 1:639-650.
14. Everitt B. Cluster Analysis 1974, Heinemann Education Books, London.
15. Festenstein R., Tolaini M., Corbella P., Mamalaki C., Parrington J., Fox M., Miliou A., Jones M., Kioussis D. Locus control region function and heterochromatin-induced position effect variegation. Science (New York, N.Y.) 1996, 271:1123-1125.
16. Figueroa B., Ailor E., Osborne D., Hardwick J.M., Reff M., Betenbaugh M.J. Enhanced cell culture performance using inducible anti-apoptotic genes E1b-19k and aven in the production of a monoclonal antibody with Chinese hamster ovary cells. Biotechnology and Bioengineering 2007, 97:877-892.
17. Freshney R.I. Cloning and Selection. Culture of Animal Cells 2005, John Wiley & Sons, Inc., New York, USA.
18. Gaj T., Gersbach C.A., Barbas Iii C.F. Zfn, Talen, and Crispr/Cas-based methods for genome engineering. Trends in Biotechnology 2013, 31:397-405.
19. Hu, W.-S., 2012. Cell Culture Bioprocess Engineering. http://www.Cellprocessbook.Com/,%20Http:/Cbt.Umn.Edu/.
20. Kantardjieff A., Jacob N.M., Yee J.C., Epstein E., Kok Y.-J., Philp R., Betenbaugh M., Hu W.-S. Transcriptome and proteome analysis of Chinese hamster ovary cells under low Temperature and butyrate treatment. Journal of Biotechnology 2010, 145:143-159.
21. Kantardjieff A., Seth G., Mcivor S., Hu W.-S. Genetic Manipulations Of Mammalian Cells For Protein Expression. Manual of Industrial Microbiology and Biotechnology 2010, 330-344. American Society For Microbiology (Asm). 3rd Ed. R.H. Baltz, J.E. Davies, A.L. Demain (Eds.).
22. Kaufmann H., Fussenegger M. Metabolic Engineering Of Mammalian Cells For Higher Protein Yield. New Comprehensive Biochemistry 2003, vol. 38:457-469. Elsevier.
23. Keeler K.J., Dray T., Penney J.E., Gloor G.B. Gene targeting of a plasmid-borne sequence to a double-strand dna break in Drosophila melanogaster. Molecular And Cellular Biology 1996, 16:522-528.
24. Kim J.Y., Kim Y.G., Lee G.M. Cho cells in biotechnology for production of recombinant proteins: current state and further potential. Applied Microbiology And Biotechnology 2012, 93:917-930.
25. Kleinjan D.-J., Van Heyningen V. Position effect in human genetic disease. Human Molecular Genetics 1998, 7:1611-1618.
26. Le H., Kabbur S., Pollastrini L., Sun Z., Mills K., Johnson K., Karypis G., Hu W.-S. Multivariate analysis of cell culture bioprocess data-lactate consumption as process indicator. Journal of Biotechnology 2012, 162:210-223.
27. Leader B., Baca Q.J., Golan D.E. Protein therapeutics: a summary and pharmacological classification. Nature Reviews Drug Discovery 2008, 7:21-39.
28. Mali P., Yang L., Esvelt K.M., Aach J., Guell M., Dicarlo J.E., Norville J.E., Church G.M. RNA-guided human genome engineering via Cas9. Science 2013, 339:823-826.
29. Mehra S., Lian W., Jayapal K., Charaniya S., Sherman D., Hu W.-S. A framework to analyze multiple time series data: a case study with streptomyces coelicolor. Journal of Industrial Microbiology and Biotechnology 2006, 33:159-172.
30. Meleady P., Doolan P., Henry M., Barron N., Keenan J., O'sullivan F., Clarke C., Gammell P., Melville M., 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.
31. Miller J.C., Tan S., Qiao G., Barlow K.A., Wang J., Xia D.F., Meng X., Paschon D.E., Leung E., Hinkley S.J., Dulay G.P., Hua K.L., Ankoudinova I., Cost G.J., Urnov F.D., Zhang H.S., Holmes M.C., Zhang L., Gregory P.D., Rebar E.J. A tale nuclease architecture for efficient genome editing. Nature Biotechnology 2011, 29:143-148.
32. Minn A.H. Thioredoxin-interacting protein is stimulated by glucose through a carbohydrate response element and induces beta cell apoptosis. Endocrinology 2005, 146:2397-2405.
33. Mussolino C., Morbitzer R., Lutge F., Dannemann N., Lahaye T., Cathomen T. A novel tale nuclease scaffold enables high genome editing activity in combination with low toxicity. Nucleic Acids Research 2011, 39:9283-9293.
34. Nivitchanyong T., Martinez A., Ishaque A., Murphy J.E., Konstantinov K., Betenbaugh M.J., Thrift J. Anti-apoptotic genes aven and e1b-19k enhance performance of Bhk cells engineered to express recombinant factor viii in batch and low perfusion cell culture. Biotechnology and Bioengineering 2007, 98:825-841.
35. Seth G., Charaniya S., Wlaschin K., Hu W. In pursuit of a super producer-alternative paths to high producing recombinant mammalian cells. Current Opinion in Biotechnology 2007, 18:557-564.
36. Seth G., Hossler P., Yee J., Hu W.-S. Engineering Cells for Cell culture Bioprocessing - Physiological Fundamentals Cell Culture Engineering 2006, vol. 101:119-164. Springer, Berlin/Heidelberg.
37. Soukas A., Socci N.D., Saatkamp B.D., Novelli S., Friedman J.M. Distinct transcriptional profiles of adipogenesisin vivo and in vitro. Journal of Biological Chemistry 2001, 276:34167-34174.
38. Suzuki H., Forrest A.R.R., Van Nimwegen E., Daub C.O., Balwierz P.J., Irvine K.M., Lassmann T., Ravasi T., Hasegawa Y., De Hoon M.J.L., Katayama S., Schroder K., Carninci P., Tomaru Y., Kanamori-Katayama M., Kubosaki A., Akalin A., Ando Y., Arner E., Asada M., Asahara H., Bailey T., Bajic V.B., Bauer D., Beckhouse A.G., Bertin N., Björkegren J., Brombacher F., Bulger E., Chalk A.M., Chiba J., Cloonan N., Dawe A., Dostie J., Engström P.G., Essack M., Faulkner G.J., Fink J.L., Fredman D., Fujimori K., Furuno M., Gojobori T., Gough J., Grimmond S.M., Gustafsson M., Hashimoto M., Hashimoto T., Hatakeyama M., Heinzel S., Hide W., Hofmann O., Hörnquist M., Huminiecki L., Ikeo K., Imamoto N., Inoue S., Inoue Y., Ishihara R., Iwayanagi T., Jacobsen A., Kaur M., Kawaji H., Kerr M.C., Kimura R., Kimura S., Kimura Y., Kitano H., Koga H., Kojima T., Kondo S., Konno T., Krogh A., Kruger A., Kumar A., Lenhard B., Lennartsson A., Lindow M., Lizio M., Macpherson C., Maeda N., Maher C.A., Maqungo M., Mar J., Matigian N.A., Matsuda H., Mattick J.S., Meier S., Miyamoto S., Miyamoto-Sato E., Nakabayashi K., Nakachi Y., Nakano M., Nygaard S., Okayama T., Okazaki Y., Okuda-Yabukami H., Orlando V., Otomo J., Pachkov M., Petrovsky N., Plessy C., Quackenbush J., Radovanovic A., Rehli M., Saito R., Sandelin A., Schmeier S., Schönbach C., Schwartz A.S., Semple C.A., Sera M., Severin J., Shirahige K., Simons C., St.Laurent G., Suzuki M., Suzuki T., Sweet M.J., Taft R.J., Takeda S., Takenaka Y., Tan K., Taylor M.S., Teasdale R.D., Tegnér J., Teichmann S., Valen E., Wahlestedt C., Waki K., Waterhouse A., Wells C.A., Winther O., Wu L., Yamaguchi K., Yanagawa H., Yasuda J., Zavolan M., Hume D.A., Arakawa T., Fukuda S., Imamura K., Kai C., Kaiho A., Kawashima T., Kawazu C., Kitazume Y., Kojima M., Miura H., Murakami K., Murata M., Ninomiya N., Nishiyori H., Noma S., Ogawa C., Sano T., Simon C., Tagami M., Takahashi Y., Kawai J., Hayashizaki Y. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics 2009, 41:553-562.
39. Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676.
40. Thaisuchat H., Baumann M., Pontiller J., Hesse F., Ernst W. Identification of a novel temperature sensitive promoter in Cho cells. Bmc Biotechnology 2011, 11:51.
41. Tigges M., Fussenegger M. Xbp1-based engineering of secretory capacity enhances the productivity of Chinese hamster ovary cells. Metabolic Engineering 2006, 8:264-272.
42. Ulloa-Montoya F., Kidder B., Pauwelyn K., Chase L., Luttun A., Crabbe A., Geraerts M., Sharov A., Piao Y., Ko M., Hu W.-S., Verfaillie C. Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity. Genome Biology 2007, 8:R163.
43. Urnov F.D., Miller J.C., Lee Y.L., Beausejour C.M., Rock J.M., Augustus S., Jamieson A.C., Porteus M.H., Gregory P.D., Holmes M.C. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 2005, 435:646-651.
44. Urnov F.D., Rebar E.J., Holmes M.C., Zhang H.S., Gregory P.D. Genome editing with engineered zinc finger nucleases. Nature Reviews Genetics 2010, 11:636-646.
45. Wang Z., Rong Y.P., Malone M.H., Davis M.C., Zhong F., Distelhorst C.W. Thioredoxin-interacting protein (Txnip) is a glucocorticoid-regulated primary response gene involved in mediating glucocorticoid-induced apoptosis. Oncogene 2005, 25:1903-1913.
46. Weber W., Fussenegger M. Inducible product gene expression technology tailored to bioprocess engineering. Current Opinion in Biotechnology 2007.
47. Wirth M., Hauser H. Genetic engineering of animal cells. Biotechnology 2008, 662-744. Wiley-Vch Verlag Gmbh, Weinheim, Germany.
48. Wlaschin K.F., Hu W.-S. Engineering cell metabolism for high-density cell culture via manipulation of sugar transport. Journal of Biotechnology 2007, 131:168-176.
49. Wurm F.M. Production of recombinant protein therapeutics in cultivated mammalian cells. Nature Biotechnology 2004, 22:1393-1398.
50. Xu X., Nagarajan H., Lewis N.E., Pan S., Cai Z., Liu X., Chen W., Xie M., Wang W., Hammond S., Andersen M.R., Neff N., Passarelli B., Koh W., Fan H.C., Wang J., Gui Y., Lee K.H., Betenbaugh M.J., Quake S.R., Famili I., Palsson B.O., Wang J. The genomic sequence of the Chinese hamster ovary (Cho)-K1 cell line. Nature Biotechnology 2011, 29:735-741.
51. Zhang Y., Hatch K., Bacon J., Wernisch L. An integrated machine learning approach for predicting Dosr-regulated genes in Mycobacterium tuberculosis. Bmc Systems Biology 2010, 4:37.
52. Zhou M., Crawford Y., Ng D., Tung J., Pynn A.F.J., Meier A., Yuk I.H., Vijayasankaran N., Leach K., Joly J., Snedecor B., Shen A. Decreasing lactate level and increasing antibody production in Chinese hamster ovary cells (Cho) by reducing the expression of lactate dehydrogenase and pyruvate dehydrogenase kinases. Journal of Biotechnology 2011, 153:27-34.