Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.)

Becker J, Timmermann C, Rupp O, Albaum S, Brinkrolf K, Goesmann A, Pühler A, Tauch A, Noll T (2014)
Journal of biotechnology 178: 23-31.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Becker, JenniferUniBi; Timmermann, ChristinaUniBi; Rupp, OliverUniBi; Albaum, StefanUniBi ; Brinkrolf, KarinaUniBi; Goesmann, AlexanderUniBi ; Pühler, AlfredUniBi ; Tauch, AndreasUniBi; Noll, ThomasUniBi
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe T. Noll
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Graduate Center > Graduate Cluster Industrial Biotechnology
Technische Fakultät > AG Fermentationstechnik
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Technische Fakultät > AG Zellkulturtechnik
Centrum für Biotechnologie > Arbeitsgruppe A. Tauch
Abstract / Bemerkung
The increasing importance of Chinese hamster ovary (CHO) cells for the production of pharmaceutical proteins has awakened the demand to understand the cellular metabolism of these cells. However, satisfactory gene expression studies have yet been impractical due to insufficient coverage of sequences. In this work, previously determined sequence information of CHO cells and newly derived data from 454 and Illumina sequencing was used to establish the CHO41K microarray which contains 41,304 probes. Self-hybridisation was performed for replica determination and samples were run in triplicates to increase statistical power. For determination of technical variance, confidence intervals at an M-value of ±0.6 for 95% and at ±2.3 for 99% of the probes were calculated. Intra-microarray and slide to slide variance was not detectable. In a first application, this microarray enabled an in-depth look inside the cellular transcriptome of CHO cells cultured in the presence or absence of the growth supporting substance "insulin like growth factor 1" (IGF-1) analogue LongR(3). Its effect on the cells ranged from enhanced growth to delay of cell death as well as cytoskeletal installation. Suggesting that under supplementation, a minimised cellular effort in installation of a large cytoskeleton occurs, possibly in favour of promoting faster cell division.
Erscheinungsjahr
2014
Zeitschriftentitel
Journal of biotechnology
Band
178
Seite(n)
23-31
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/2676552

Zitieren

Becker J, Timmermann C, Rupp O, et al. Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.). Journal of biotechnology. 2014;178:23-31.
Becker, J., Timmermann, C., Rupp, O., Albaum, S., Brinkrolf, K., Goesmann, A., Pühler, A., et al. (2014). Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.). Journal of biotechnology, 178, 23-31. doi:10.1016/j.jbiotec.2014.02.021
Becker, Jennifer, Timmermann, Christina, Rupp, Oliver, Albaum, Stefan, Brinkrolf, Karina, Goesmann, Alexander, Pühler, Alfred, Tauch, Andreas, and Noll, Thomas. 2014. “Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.)”. Journal of biotechnology 178: 23-31.
Becker, J., Timmermann, C., Rupp, O., Albaum, S., Brinkrolf, K., Goesmann, A., Pühler, A., Tauch, A., and Noll, T. (2014). Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.). Journal of biotechnology 178, 23-31.
Becker, J., et al., 2014. Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.). Journal of biotechnology, 178, p 23-31.
J. Becker, et al., “Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.)”, Journal of biotechnology, vol. 178, 2014, pp. 23-31.
Becker, J., Timmermann, C., Rupp, O., Albaum, S., Brinkrolf, K., Goesmann, A., Pühler, A., Tauch, A., Noll, T.: Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.). Journal of biotechnology. 178, 23-31 (2014).
Becker, Jennifer, Timmermann, Christina, Rupp, Oliver, Albaum, Stefan, Brinkrolf, Karina, Goesmann, Alexander, Pühler, Alfred, Tauch, Andreas, and Noll, Thomas. “Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.)”. Journal of biotechnology 178 (2014): 23-31.

8 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A Comparative Transcriptomics Workflow for Analyzing Microarray Data From CHO Cell Cultures.
Chen C, Le H, Follstad B, Goudar CT., Biotechnol J 13(3), 2018
PMID: 29215210
Meta-Analysis of Publicly Available Chinese Hamster Ovary (CHO) Cell Transcriptomic Datasets for Identifying Engineering Targets to Enhance Recombinant Protein Yields.
Tamošaitis L, Smales CM., Biotechnol J 13(10), 2018
PMID: 29917317
Integrative analysis of DNA methylation and gene expression in butyrate-treated CHO cells.
Wippermann A, Rupp O, Brinkrolf K, Hoffrogge R, Noll T., J Biotechnol 257(), 2017
PMID: 27890772
Transcriptomic changes in CHO cells after adaptation to suspension growth in protein-free medium analysed by a species-specific microarray.
Shridhar S, Klanert G, Auer N, Hernandez-Lopez I, Kańduła MM, Hackl M, Grillari J, Stralis-Pavese N, Kreil DP, Borth N., J Biotechnol 257(), 2017
PMID: 28302587
Precision control of recombinant gene transcription for CHO cell synthetic biology.
Brown AJ, James DC., Biotechnol Adv 34(5), 2016
PMID: 26721629
The DNA methylation landscape of Chinese hamster ovary (CHO) DP-12 cells.
Wippermann A, Rupp O, Brinkrolf K, Hoffrogge R, Noll T., J Biotechnol 199(), 2015
PMID: 25701679
The GalNAc-type O-Glycoproteome of CHO cells characterized by the SimpleCell strategy.
Yang Z, Halim A, Narimatsu Y, Jitendra Joshi H, Steentoft C, Schjoldager KT, Alder Schulz M, Sealover NR, Kayser KJ, Paul Bennett E, Levery SB, Vakhrushev SY, Clausen H., Mol Cell Proteomics 13(12), 2014
PMID: 25092905
Hypoxia influences protein transport and epigenetic repression of CHO cell cultures in shake flasks.
Qian Y, Xing Z, Lee S, Mackin NA, He A, Kayne PS, He Q, Qian NX, Li ZJ., Biotechnol J 9(11), 2014
PMID: 25271019

33 References

Daten bereitgestellt von Europe PubMed Central.

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712

Bahr, 2009
Initial transcriptome and proteome analyses of low culture temperature-induced expression in CHO cells producing erythropoietin.
Baik JY, Lee MS, An SR, Yoon SK, Joo EJ, Kim YH, Park HW, Lee GM., Biotechnol. Bioeng. 93(2), 2006
PMID: 16187333
Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing.
Becker J, Hackl M, Rupp O, Jakobi T, Schneider J, Szczepanowski R, Bekel T, Borth N, Goesmann A, Grillari J, Kaltschmidt C, Noll T, Puhler A, Tauch A, Brinkrolf K., J. Biotechnol. 156(3), 2011
PMID: 21945585
Methods for off-line analysis of nutrients and products in mammalian cell culture
Büntemeyer, 2007
The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.
Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT., Clin. Chem. 55(4), 2009
PMID: 19246619
Predicting cell-specific productivity from CHO gene expression.
Clarke C, Doolan P, Barron N, Meleady P, O'Sullivan F, Gammell P, Melville M, Leonard M, Clynes M., J. Biotechnol. 151(2), 2010
PMID: 21115077
Comparative transcriptional analysis of mouse hybridoma and recombinant Chinese hamster ovary cells undergoing butyrate treatment.
De Leon Gatti M, Wlaschin KF, Nissom PM, Yap M, Hu WS., J. Biosci. Bioeng. 103(1), 2007
PMID: 17298905
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
Transcriptional profiling of gene expression changes in a PACE-transfected CHO DUKX cell line secreting high levels of rhBMP-2.
Doolan P, Melville M, Gammell P, Sinacore M, Meleady P, McCarthy K, Francullo L, Leonard M, Charlebois T, Clynes M., Mol. Biotechnol. 39(3), 2008
PMID: 18240028
Insulin and IGF-1 induce different patterns of gene expression in mouse fibroblast NIH-3T3 cells: identification by cDNA microarray analysis.
Dupont J, Khan J, Qu BH, Metzler P, Helman L, LeRoith D., Endocrinology 142(11), 2001
PMID: 11606465
Evaluation of a genomics platform for cross-species transcriptome analysis of recombinant CHO cells.
Ernst W, Trummer E, Mead J, Bessant C, Strelec H, Katinger H, Hesse F., Biotechnol J 1(6), 2006
PMID: 16892312
ANTIBODY-SUPPRESSIBLE AND NONSUPPRESSIBLE INSULIN-LIKE ACTIVITIES IN HUMAN SERUM AND THEIR PHYSIOLOGIC SIGNIFICANCE. AN INSULIN ASSAY WITH ADIPOSE TISSUE OF INCREASED PRECISION AND SPECIFICITY.
FROESCH ER, BUERGI H, RAMSEIER EB, BALLY P, LABHART A., J. Clin. Invest. 42(), 1963
PMID: 14083170
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
Huang da W, Sherman BT, Lempicki RA., Nucleic Acids Res. 37(1), 2008
PMID: 19033363
Developing genomic platforms for Chinese hamster ovary cells.
Kantardjieff A, Nissom PM, Chuah SH, Yusufi F, Jacob NM, Mulukutla BC, Yap M, Hu WS., Biotechnol. Adv. 27(6), 2009
PMID: 19470403
Development and characterization of a Chinese hamster ovary cell-specific oligonucleotide microarray
Melville M, Doolan P, Mounts W, Barron N, Hann L, Leonard M, Clynes M, Charlebois T., Biotechnol. Lett. 33(9), 2011
PMID: IND44791534
Effects of insulin and LongR(3) on serum-free Chinese hamster ovary cell cultures expressing two recombinant proteins.
Morris AE, Schmid J., Biotechnol. Prog. 16(5), 2000
PMID: 11027158
Transcriptome and proteome profiling to understanding the biology of high productivity CHO cells.
Nissom PM, Sanny A, Kok YJ, Hiang YT, Chuah SH, Shing TK, Lee YY, Wong KT, Hu WS, Sim MY, Philp R., Mol. Biotechnol. 34(2), 2006
PMID: 17172658
Effect of medium osmolarity on hybridoma growth, metabolism, and antibody production.
Ozturk SS, Palsson BO., Biotechnol. Bioeng. 37(10), 1991
PMID: 18597326
Change of insulin-like growth factor gene expression in Chinese hamster ovary cells cultured in serum-free media
Park, Biotechnol. Bioprocess Eng. 11(), 2006
Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions.
Pearson G, Robinson F, Beers Gibson T, Xu BE, Karandikar M, Berman K, Cobb MH., Endocr. Rev. 22(2), 2001
PMID: 11294822
Genetics of somatic mammalian cells. III. Long-term cultivation of euploid cells from human and animal subjects.
PUCK TT, CIECIURA SJ, ROBINSON A., J. Exp. Med. 108(6), 1958
PMID: 13598821
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Puhler A, Noll T, Goesmann A., PLoS ONE 9(1), 2014
PMID: 24427317

AUTHOR UNKNOWN, 0
RAPYD--rapid annotation platform for yeast data.
Schneider J, Blom J, Jaenicke S, Linke B, Brinkrolf K, Neuweger H, Tauch A, Goesmann A., J. Biotechnol. 155(1), 2010
PMID: 21040748
Signalling by insulin and IGF receptors: supporting acts and new players.
Siddle K., J. Mol. Endocrinol. 47(1), 2011
PMID: 21498522
Normalization of cDNA microarray data.
Smyth GK, Speed T., Methods 31(4), 2003
PMID: 14597310
Transcriptional profiling of phenotypically different Epo-Fc expressing CHO clones by cross-species microarray analysis.
Trummer E, Ernst W, Hesse F, Schriebl K, Lattenmayer C, Kunert R, Vorauer-Uhl K, Katinger H, Muller D., Biotechnol J 3(7), 2008
PMID: 18481264
The Universal Protein Resource (UniProt).
UniProt Consortium., Nucleic Acids Res. 35(Database issue), 2006
PMID: 17142230
EST sequencing for gene discovery in Chinese hamster ovary cells.
Wlaschin KF, Nissom PM, Gatti Mde L, Ong PF, Arleen S, Tan KS, Rink A, Cham B, Wong K, Yap M, Hu WS., Biotechnol. Bioeng. 91(5), 2005
PMID: 16003777
Transcriptional profiling of apoptotic pathways in batch and fed-batch CHO cell cultures.
Wong DC, Wong KT, Lee YY, Morin PN, Heng CK, Yap MG., Biotechnol. Bioeng. 94(2), 2006
PMID: 16570314
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.
Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S, Andersen MR, Neff N, Passarelli B, Koh W, Fan HC, Wang J, Gui Y, Lee KH, Betenbaugh MJ, Quake SR, Famili I, Palsson BO, Wang J., Nat. Biotechnol. 29(8), 2011
PMID: 21804562
Genomic and proteomic exploration of CHO and hybridoma cells under sodium butyrate treatment.
Yee JC, de Leon Gatti M, Philp RJ, Yap M, Hu WS., Biotechnol. Bioeng. 99(5), 2008
PMID: 17929327
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 24613301
PubMed | Europe PMC

Suchen in

Google Scholar