151
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Yeo JHM, Ho SCL, Mariati M, Koh E, Tay SJ, Woen S, Zhang P, Yang Y. Optimized Selection Marker and CHO Host Cell Combinations for Generating High Monoclonal Antibody Producing Cell Lines. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700175] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 09/13/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Jessna H. M. Yeo
- Bioprocessing Technology Institute; Agency for Science; Technology and Research (A*STAR) Singapore Singapore
| | - Steven C. L. Ho
- Bioprocessing Technology Institute; Agency for Science; Technology and Research (A*STAR) Singapore Singapore
| | - Mariati Mariati
- Bioprocessing Technology Institute; Agency for Science; Technology and Research (A*STAR) Singapore Singapore
| | - Esther Koh
- Bioprocessing Technology Institute; Agency for Science; Technology and Research (A*STAR) Singapore Singapore
| | - Shi Jie Tay
- Bioprocessing Technology Institute; Agency for Science; Technology and Research (A*STAR) Singapore Singapore
| | - Susanto Woen
- Bioprocessing Technology Institute; Agency for Science; Technology and Research (A*STAR) Singapore Singapore
| | - Peiqing Zhang
- Bioprocessing Technology Institute; Agency for Science; Technology and Research (A*STAR) Singapore Singapore
| | - Yuansheng Yang
- Bioprocessing Technology Institute; Agency for Science; Technology and Research (A*STAR) Singapore Singapore
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152
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Heffner KM, Hizal DB, Yerganian GS, Kumar A, Can Ö, O’Meally R, Cole R, Chaerkady R, Wu H, Bowen MA, Betenbaugh MJ. Lessons from the Hamster: Cricetulus griseus Tissue and CHO Cell Line Proteome Comparison. J Proteome Res 2017; 16:3672-3687. [DOI: 10.1021/acs.jproteome.7b00382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | | | - Amit Kumar
- Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Özge Can
- Acibadem University, Medical Biochemistry, Istanbul, Maltepe, Turkey
| | - Robert O’Meally
- Johns Hopkins Medical Institute, Baltimore, Maryland 21205, United States
| | - Robert Cole
- Johns Hopkins Medical Institute, Baltimore, Maryland 21205, United States
| | | | - Herren Wu
- MedImmune, Gaithersburg, Maryland 20878, United States
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153
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Shen CC, Sung LY, Lin SY, Lin MW, Hu YC. Enhancing Protein Production Yield from Chinese Hamster Ovary Cells by CRISPR Interference. ACS Synth Biol 2017; 6:1509-1519. [PMID: 28418635 DOI: 10.1021/acssynbio.7b00020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chinese hamster ovary (CHO) cells are an important host for biopharmaceutical production. Generation of stable CHO cells typically requires cointegration of dhfr and a foreign gene into chromosomes and subsequent methotrexate (MTX) selection for coamplification of dhfr and foreign gene. CRISPR interference (CRISPRi) is an emerging system that effectively suppresses gene transcription through the coordination of dCas9 protein and guide RNA (gRNA). However, CRISPRi has yet to be exploited in CHO cells. Here we constructed vectors expressing the functional CRISPRi system and proved effective CRISPRi-mediated suppression of dhfr transcription in CHO cells. We next generated stable CHO cell clones coexpressing DHFR, the model protein (EGFP), dCas9 and gRNA targeting dhfr. Combined with MTX selection, CRISPRi-mediated repression of dhfr imparted extra selective pressure to force CHO cells to coamplify more copies of dhfr and egfp genes. Compared with the traditional method relying on MTX selection (up to 250 nM), the CRISPRi approach increased the dhfr copy number ∼3-fold, egfp copy number ∼3.6-fold and enhanced the EGFP expression ∼3.8-fold, without impeding the cell growth. Furthermore, we exploited the CRISPRi approach to enhance the productivity of granulocyte colony stimulating factor (G-CSF) ∼2.3-fold. Our data demonstrate, for the first time, the application of CRISPRi in CHO cells to enhance recombinant protein production and may pave a new avenue to CHO cell engineering.
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Affiliation(s)
- Chih-Che Shen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Li-Yu Sung
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Shih-Yeh Lin
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Mei-Wei Lin
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
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154
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Baumann M, Gludovacz E, Sealover N, Bahr S, George H, Lin N, Kayser K, Borth N. Preselection of recombinant gene integration sites enabling high transcription rates in CHO cells using alternate start codons and recombinase mediated cassette exchange. Biotechnol Bioeng 2017; 114:2616-2627. [DOI: 10.1002/bit.26388] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/13/2017] [Accepted: 07/19/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB); Graz Austria
| | | | | | - Scott Bahr
- MilliporeSigma (SAFC); St. Louis Minnesota
| | | | - Nan Lin
- MilliporeSigma (SAFC); St. Louis Minnesota
| | | | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (ACIB); Graz Austria
- University of Natural Resources and Life Sciences (BOKU); Vienna Austria
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155
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Brown AJ, Kalsi D, Fernandez-Martell A, Cartwright J, Barber NOW, Patel YD, Turner R, Bryant CL, Johari YB, James DC. Expression Systems for Recombinant Biopharmaceutical Production by Mammalian Cells in Culture. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1002/9783527699124.ch13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Adam J. Brown
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Devika Kalsi
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | | | - Joe Cartwright
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Nicholas O. W. Barber
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Yash D. Patel
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | | | - Claire L. Bryant
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - Yusuf B. Johari
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
| | - David C. James
- University of Sheffield; Department of Chemical and Biological Engineering; Mappin St. Sheffield S1 3JD UK
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156
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Park JH, Jin JH, Ji IJ, An HJ, Kim JW, Lee GM. Proteomic analysis of host cell protein dynamics in the supernatant of Fc-fusion protein-producing CHO DG44 and DUKX-B11 cell lines in batch and fed-batch cultures. Biotechnol Bioeng 2017. [DOI: 10.1002/bit.26360] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jin Hyoung Park
- Department of Biological Sciences; KAIST; 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
| | - Jong Hwa Jin
- New Drug Development Center; Cheongju-si Chungbuk Republic of Korea
| | - In Jung Ji
- Graduate School of Analytical Science & Technology; Chungnam National University; Daejon Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science & Technology; Chungnam National University; Daejon Republic of Korea
| | - Jong Won Kim
- New Drug Development Center; Cheongju-si Chungbuk Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences; KAIST; 291 Daehak-ro, Yuseong-gu Daejeon 34141 Republic of Korea
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157
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Abstract
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These “fingerprints” of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility.
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158
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Richelle A, Lewis NE. Improvements in protein production in mammalian cells from targeted metabolic engineering. ACTA ACUST UNITED AC 2017; 6:1-6. [PMID: 29104947 DOI: 10.1016/j.coisb.2017.05.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bioprocess optimization has yielded powerful clones for biotherapeutic production. However, new genomic technologies allow more targeted approaches to cell line development. Here we review efforts to enhance protein production in mammalian cells through metabolic engineering. Most efforts aimed to reduce toxic byproducts accumulation to enhance protein productivity. However, recent work highlights the possibility of regulating other desirable traits (e.g., apoptosis and glycosylation) by targeting central metabolism since these processes are interconnected. Therefore, as we further detail the pathways underlying cell growth and protein production and deploy diverse algorithms for their analysis, opportunities will arise to move beyond simple cell line designs and facilitate cell engineering strategies with complex combinations of genes that together underlie a phenotype of interest.
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Affiliation(s)
- Anne Richelle
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States.,Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States
| | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States.,Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States
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159
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López-López D, Gómez-Nieto R, Herrero-Turrión MJ, García-Cairasco N, Sánchez-Benito D, Ludeña MD, López DE. Overexpression of the immediate-early genes Egr1, Egr2, and Egr3 in two strains of rodents susceptible to audiogenic seizures. Epilepsy Behav 2017; 71:226-237. [PMID: 26775236 DOI: 10.1016/j.yebeh.2015.12.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 12/10/2015] [Accepted: 12/12/2015] [Indexed: 11/17/2022]
Abstract
Genetic animal models of epilepsy are an important tool for further understanding the basic cellular mechanisms underlying epileptogenesis and for developing novel antiepileptic drugs. We conducted a comparative study of gene expression in the inferior colliculus, a nucleus that triggers audiogenic seizures, using two animal models, the Wistar audiogenic rat (WAR) and the genetic audiogenic seizure hamster (GASH:Sal). For this purpose, both models were exposed to high intensity auditory stimulation, and 60min later, the inferior colliculi were collected. As controls, intact Wistar rats and Syrian hamsters were subjected to stimulation and tissue preparation protocols identical to those performed on the experimental animals. Ribonucleic acid was isolated, and microarray analysis comparing the stimulated Wistar and WAR rats showed that the genomic profile of these animals displayed significant (fold change, |FC|≥2.0 and p<0.05) upregulation of 38 genes and downregulation of 47 genes. Comparison of gene expression profiles between stimulated control hamsters and stimulated GASH:Sal revealed the upregulation of 10 genes and the downregulation of 5 genes. Among the common genes that were altered in both models, we identified the zinc finger immediate-early growth response gene Egr3. The Egr3 protein is a transcription factor that is induced by distinct stress-elicited factors. Based on immunohistochemistry, this protein was expressed in the cochlear nucleus complex, the inferior colliculus, and the hippocampus of both animal models as well as in lymphoma tumors of the GASH:Sal. Our results support that the overexpression of the Egr3 gene in both models might contribute to neuronal viability and development of lymphoma in response to stress associated with audiogenic seizures. This article is part of a Special Issue entitled "Genetic and Reflex Epilepsies, Audiogenic Seizures and Strains: From Experimental Models to the Clinic".
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Affiliation(s)
- D López-López
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain
| | - R Gómez-Nieto
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain; Department of Cell Biology and Pathology, School of Medicine, University of Salamanca, Salamanca, Spain
| | - M J Herrero-Turrión
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain
| | - N García-Cairasco
- Physiology Department, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, Brazil
| | - D Sánchez-Benito
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain
| | - M D Ludeña
- Department of Cell Biology and Pathology, School of Medicine, University of Salamanca, Salamanca, Spain
| | - D E López
- Institute for Neuroscience of Castilla y León (INCyL), University of Salamanca, Salamanca, Spain; Salamanca Institute for Biomedical Research (IBSAL), Spain; Department of Cell Biology and Pathology, School of Medicine, University of Salamanca, Salamanca, Spain.
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160
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Lalonde ME, Durocher Y. Therapeutic glycoprotein production in mammalian cells. J Biotechnol 2017; 251:128-140. [DOI: 10.1016/j.jbiotec.2017.04.028] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 04/12/2017] [Accepted: 04/23/2017] [Indexed: 12/12/2022]
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161
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Kreimer S, Gao Y, Ray S, Jin M, Tan Z, Mussa NA, Tao L, Li Z, Ivanov AR, Karger BL. Host Cell Protein Profiling by Targeted and Untargeted Analysis of Data Independent Acquisition Mass Spectrometry Data with Parallel Reaction Monitoring Verification. Anal Chem 2017; 89:5294-5302. [PMID: 28402653 DOI: 10.1021/acs.analchem.6b04892] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Host cell proteins (HCPs) are process-related impurities of biopharmaceuticals that remain at trace levels despite multiple stages of downstream purification. Currently, there is interest in implementing LC-MS in biopharmaceutical HCP profiling alongside conventional ELISA, because individual species can be identified and quantitated. Conventional data dependent LC-MS is hampered by the low concentration of HCP-derived peptides, which are 5-6 orders of magnitude less abundant than the biopharmaceutical-derived peptides. In this paper, we present a novel data independent acquisition (DIA)-MS workflow to identify HCP peptides using automatically combined targeted and untargeted data processing, followed by verification and quantitation using parallel reaction monitoring (PRM). Untargeted data processing with DIA-Umpire provided a means of identifying HCPs not represented in the assay library used for targeted, peptide-centric, data analysis. An IgG1 monoclonal antibody (mAb) purified by Protein A column elution, cation exchange chromatography, and ultrafiltration was analyzed using the workflow with 1D-LC. Five protein standards added at 0.5 to 100 ppm concentrations were detected in the background of the purified mAb, demonstrating sensitivity to low ppm levels. A calibration curve was constructed on the basis of the summed peak areas of the three highest intensity fragment ions from the highest intensity peptide of each protein standard. Sixteen HCPs were identified and quantitated on the basis of the calibration curve over the range of low ppm to over 100 ppm in the purified mAb sample. The developed approach achieves rapid HCP profiling using 1D-LC and specific identification exploiting the high mass accuracy and resolution of the mass spectrometer.
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Affiliation(s)
- Simion Kreimer
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Yuanwei Gao
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Somak Ray
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Mi Jin
- Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States
| | - Zhijun Tan
- Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States
| | - Nesredin A Mussa
- Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States
| | - Li Tao
- Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States
| | - Zhengjian Li
- Bristol-Myers Squibb , Biologics Process and Product Development, 38 Jackson Road, Devens, Massachusetts 01434, United States
| | - Alexander R Ivanov
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Barry L Karger
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
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162
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Vishwanathan N, Bandyopadhyay A, Fu HY, Johnson KC, Springer NM, Hu WS. A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines. Biotechnol Bioeng 2017; 114:1903-1908. [DOI: 10.1002/bit.26311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/28/2017] [Accepted: 04/09/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Nandita Vishwanathan
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
| | - Arpan Bandyopadhyay
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
| | - Hsu-Yuan Fu
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
| | - Kathryn C. Johnson
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
| | - Nathan M. Springer
- Microbial and Plant Genomics Institute and Department of Plant Biology; University of Minnesota; St. Paul Minnesota
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
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163
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Orellana CA, Marcellin E, Gray PP, Nielsen LK. Overexpression of the regulatory subunit of glutamate-cysteine ligase enhances monoclonal antibody production in CHO cells. Biotechnol Bioeng 2017; 114:1825-1836. [PMID: 28436007 DOI: 10.1002/bit.26316] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 04/09/2017] [Accepted: 04/18/2017] [Indexed: 01/01/2023]
Abstract
For decades, Chinese hamster ovary (CHO) cells have been the preferred host for therapeutic monoclonal antibody (mAb) production; however, increasing mAb titer by rational engineering remains a challenge. Our previous proteomic analysis in CHO cells suggested that a higher content of glutathione (GSH) might be related to higher productivity. GSH is an important antioxidant, cell detoxifier, and is required to ensure the formation of native disulfide bonds in proteins. To investigate the involvement of GSH in mAb production, we generated stable CHO cell lines overexpressing genes involved in the first step of GSH synthesis; namely the glutamate-cysteine ligase catalytic subunit (Gclc) and the glutamate-cysteine ligase modifier subunit (Gclm). The two genes were reconstructed from our RNA-Seq de novo assembly and then were functionally annotated. Once the sequences of the genes were confirmed using proteogenomics, a transiently expressed mAb was introduced into cell lines overexpressing either Gclc or Gclm. The new cell lines were compared for mAb production to the parental cell line and changes at the proteome level were measured using SWATH. As per our previous proteomics observations, overexpressing Gclm improved productivity, titer, and the frequency of high producer clones by 70%. In contrast, overexpressing Gclc, which produced a higher amount of GSH, did not increase mAb production. We show that GSH cannot be linked to higher productivity and that Gclm may be controlling other cellular processes involved in mAb production yet to be elucidated. Biotechnol. Bioeng. 2017;114: 1825-1836. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Camila A Orellana
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter P Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
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164
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Kelly PS, Clarke C, Costello A, Monger C, Meiller J, Dhiman H, Borth N, Betenbaugh MJ, Clynes M, Barron N. Ultra-deep next generation mitochondrial genome sequencing reveals widespread heteroplasmy in Chinese hamster ovary cells. Metab Eng 2017; 41:11-22. [DOI: 10.1016/j.ymben.2017.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/31/2017] [Accepted: 02/07/2017] [Indexed: 10/20/2022]
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165
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Chen C, Le H, Goudar CT. Evaluation of two public genome references for chinese hamster ovary cells in the context of rna-seq based gene expression analysis. Biotechnol Bioeng 2017; 114:1603-1613. [PMID: 28295162 DOI: 10.1002/bit.26290] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/21/2017] [Accepted: 03/10/2017] [Indexed: 11/08/2022]
Abstract
RNA-Seq is a powerful transcriptomics tool for mammalian cell culture process development. Successful RNA-Seq data analysis requires a high quality reference for read mapping and gene expression quantification. Currently, there are two public genome references for Chinese hamster ovary (CHO) cells, the predominant mammalian cell line in the biopharmaceutical industry. In this study, we compared these two references by analyzing 60 RNA-Seq samples from a variety of CHO cell culture conditions. Among the 20,891 common genes in both references, we observed that 31.5% have more than 7.1% quantification differences, implying gene definition differences in the two references. We propose a framework to quantify this difference using two metrics, Consistency and Stringency, which account for the average quantification difference between the two references over all samples, and the sample-specific effect on the quantification result, respectively. These two metrics can be used to identify potential genes for future gene model improvement and to understand the reliability of differentially expressed genes identified by RNA-Seq data analysis. Before a more comprehensive genome reference for CHO cells emerges, the strategy proposed in this study can enable more robust transcriptome analysis from CHO cell RNA-Seq data. Biotechnol. Bioeng. 2017;114: 1603-1613. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Chun Chen
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, California, 91320
| | - Huong Le
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, California, 91320
| | - Chetan T Goudar
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, California, 91320
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166
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Gowtham YK, Saski CA, Harcum SW. Low glucose concentrations within typical industrial operating conditions have minimal effect on the transcriptome of recombinant CHO cells. Biotechnol Prog 2017; 33:771-785. [PMID: 28371311 DOI: 10.1002/btpr.2462] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/07/2017] [Indexed: 12/16/2022]
Abstract
Typically, mammalian cell culture medium contains high glucose concentrations that are analogous to diabetic levels in humans, suggesting that mammalian cells are cultivated in excessive glucose. Using RNA-Seq, this study characterized the Chinese hamster ovary (CHO) cell transcriptome under two glucose concentrations to assess the genetic effects associated with metabolic pathways, in addition to other global responses. The initial extracellular glucose concentrations used represented high (30 mM) and low (10 mM) glucose conditions, where at the time the transcriptomes were compared, the glucose concentrations were approximately 24 and 4.4 mM for the mid-exponential cultures, where 4.4 mM represents a common target concentration in the biopharmaceutical industry for controlled fed-batch cultures. A recombinant CHO cell line producing a monoclonal antibody was used, such that the impact on glycosylation genes could be evaluated. Relatively few genes were identified as being significantly different (FDR ≤ 0.01) between the high and low glucose conditions, for example, only 575 genes, and only 40 of these genes had 2-fold or greater differences. Gene expression differences for glycolysis, TCA cycle, and glycosylation-related reactions were minimal and unlikely to have biological significance. This transcriptome study indicates that low glucose concentrations in the culture medium are unlikely to cause any biologically significant or detrimental changes to CHO cells at the transcriptome level. Furthermore, it is well-known that maintaining low glucose concentrations in fed-batch cultures can reduce lactate production, which in turn improves process outcomes. Taken together, the transcriptome data supports the continued development of low glucose-based processes to control lactate. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:771-785, 2017.
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Affiliation(s)
| | - Christopher A Saski
- Inst. of Translational Genomics, Clemson University, Clemson, SC, 29634.,Dept. of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634
| | - Sarah W Harcum
- Dept. of Bioengineering, Clemson University, Clemson, SC, 29634
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167
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Muluhngwi P, Richardson K, Napier J, Rouchka EC, Mott JL, Klinge CM. Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells. Mol Cell Endocrinol 2017; 444:38-47. [PMID: 28137615 PMCID: PMC5316361 DOI: 10.1016/j.mce.2017.01.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 01/28/2023]
Abstract
miR-29b and miR-29a transcript levels were reported to increase in exponentially growing CHO-K1 cells. Here, we examine the regulation of miR-29b-1/a in CHO-K1 cells. We observed that 4-hydroxytamoxifen (4-OHT) increased pri-miR-29b-1 and pri-miR-29a transcription in CHO-K1 cells by activating endogenous estrogen receptor α (ERα). DICER, an established, bona fide target of miR-29b-1/a, was shown to be regulated by 4-OHT in CHO-K1 cells. We showed that miR-29b-1 and miR-29a serve a repressive role in cell proliferation, migration, invasion, and colony formation in CHO-K1 cells. To identify other targets of miR-29b-1 and miR-29a, RNA sequencing was performed by transfecting cells with anti-miR-29a, which inhibits both miR-29a and miR-29b-1, pre-miR-29b-1, and/or pre-miR-29a. In silico network analysis in MetaCore™ identified common and unique putative gene targets of miR-29b-1 and miR-29a. Pathway analysis of identified putative miR-29 targets were related to cell adhesion, cytoskeletal remodeling, and development. Further inquiry revealed regulation of pathways mediating responses to growth factor stimulus and cell cycle regulation.
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Affiliation(s)
- Penn Muluhngwi
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Kirsten Richardson
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Joshua Napier
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA
| | - Justin L Mott
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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168
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Lund AM, Kaas CS, Brandl J, Pedersen LE, Kildegaard HF, Kristensen C, Andersen MR. Network reconstruction of the mouse secretory pathway applied on CHO cell transcriptome data. BMC SYSTEMS BIOLOGY 2017; 11:37. [PMID: 28298216 PMCID: PMC5353859 DOI: 10.1186/s12918-017-0414-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 02/27/2017] [Indexed: 11/21/2022]
Abstract
Background Protein secretion is one of the most important processes in eukaryotes. It is based on a highly complex machinery involving numerous proteins in several cellular compartments. The elucidation of the cell biology of the secretory machinery is of great importance, as it drives protein expression for biopharmaceutical industry, a 140 billion USD global market. However, the complexity of secretory process is difficult to describe using a simple reductionist approach, and therefore a promising avenue is to employ the tools of systems biology. Results On the basis of manual curation of the literature on the yeast, human, and mouse secretory pathway, we have compiled a comprehensive catalogue of characterized proteins with functional annotation and their interconnectivity. Thus we have established the most elaborate reconstruction (RECON) of the functional secretion pathway network to date, counting 801 different components in mouse. By employing our mouse RECON to the CHO-K1 genome in a comparative genomic approach, we could reconstruct the protein secretory pathway of CHO cells counting 764 CHO components. This RECON furthermore facilitated the development of three alternative methods to study protein secretion through graphical visualizations of omics data. We have demonstrated the use of these methods to identify potential new and known targets for engineering improved growth and IgG production, as well as the general observation that CHO cells seem to have less strict transcriptional regulation of protein secretion than healthy mouse cells. Conclusions The RECON of the secretory pathway represents a strong tool for interpretation of data related to protein secretion as illustrated with transcriptomic data of Chinese Hamster Ovary (CHO) cells, the main platform for mammalian protein production. Electronic supplementary material The online version of this article (doi:10.1186/s12918-017-0414-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne Mathilde Lund
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kgs. Lyngby, Denmark
| | - Christian Schrøder Kaas
- Recombinant Expression Technologies, Global Research Unit, Novo Nordisk A/S, Novo Nordisk Park, DK-2760, Måløv, Denmark
| | - Julian Brandl
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kgs. Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, DK-2800, Kgs. Lyngby, Denmark
| | - Claus Kristensen
- Faculty of Health and Medical Sciences, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200, København N, Denmark
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, DK-2800, Kgs. Lyngby, Denmark.
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169
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Park JH, Jin JH, Lim MS, An HJ, Kim JW, Lee GM. Proteomic Analysis of Host Cell Protein Dynamics in the Culture Supernatants of Antibody-Producing CHO Cells. Sci Rep 2017; 7:44246. [PMID: 28281648 PMCID: PMC5345005 DOI: 10.1038/srep44246] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 02/06/2017] [Indexed: 12/21/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are the most common cell line used for the production of therapeutic proteins including monoclonal antibodies (mAbs). Host cell proteins (HCPs), secreted and released from lysed cells, accumulate extracellularly during the cultures of recombinant CHO (rCHO) cells, potentially impairing product quality. In an effort to maintain good mAb quality during the cultures, HCPs accumulated extracellularly in batch and fed-batch cultures of a mAb-producing rCHO cell line were identified and quantified by nanoflow liquid chromatography-tandem mass spectrometry, followed by their gene ontology and functional analysis. Due to higher cell concentration and longer culture duration, more HCPs were identified and quantitated in fed-batch culture (2145 proteins identified and 1673 proteins quantified) than in batch culture (1934 proteins identified and 1486 proteins quantified). Clustering analysis of HCPs showed that the concentration profiles of HCPs affecting mAb quality (Lgmn, Ctsd, Gbl1, and B4galt1) correlated with changes in mAb quality attributes such as aggregation, charge variants, and N-glycosylation during the cultures. Taken together, the dataset of HCPs obtained in this study provides insights into determining the appropriate target proteins to be removed during both the cultures and purification steps for ensuring good mAb quality.
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Affiliation(s)
- Jin Hyoung Park
- Department of Biological Sciences, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jong Hwa Jin
- New Drug Development Center, 123 Osongsaengmyeng-ro, Cheongju-si, Chungbuk 28160, Republic of Korea
| | - Myung Sin Lim
- New Drug Development Center, 123 Osongsaengmyeng-ro, Cheongju-si, Chungbuk 28160, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science &Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejon 34134, Republic of Korea
| | - Jong Won Kim
- New Drug Development Center, 123 Osongsaengmyeng-ro, Cheongju-si, Chungbuk 28160, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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170
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Application of 13C flux analysis to identify high-productivity CHO metabolic phenotypes. Metab Eng 2017; 43:218-225. [PMID: 28122259 DOI: 10.1016/j.ymben.2017.01.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/09/2016] [Accepted: 01/19/2017] [Indexed: 02/07/2023]
Abstract
Industrial bioprocesses place high demands on the energy metabolism of host cells to meet biosynthetic requirements for maximal protein expression. Identifying metabolic phenotypes that promote high expression is therefore a major goal of the biotech industry. We conducted a series of 13C flux analysis studies to examine the metabolic response to IgG expression during early stationary phase of CHO cell cultures grown in 3L fed-batch bioreactors. We examined eight clones expressing four different IgGs and compared with three non-expressing host-cell controls. Some clones were genetically manipulated to be apoptosis-resistant by expressing Bcl-2Δ, which correlated with increased IgG production and elevated glucose metabolism. The metabolic phenotypes of the non-expressing, IgG-expressing, and Bcl-2Δ/IgG-expressing clones were fully segregated by hierarchical clustering analysis. Lactate consumption and citric acid cycle fluxes were most strongly associated with specific IgG productivity. These studies indicate that enhanced oxidative metabolism is a characteristic of high-producing CHO cell lines.
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171
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Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion. Sci Rep 2017; 7:40388. [PMID: 28091612 PMCID: PMC5238448 DOI: 10.1038/srep40388] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/05/2016] [Indexed: 12/22/2022] Open
Abstract
Recombinant protein production coopts the host cell machinery to provide high protein yields of industrial enzymes or biotherapeutics. However, since protein translation is energetically expensive and tightly controlled, it is unclear if highly expressed recombinant genes are translated as efficiently as host genes. Furthermore, it is unclear how the high expression impacts global translation. Here, we present the first genome-wide view of protein translation in an IgG-producing CHO cell line, measured with ribosome profiling. Through this we found that our recombinant mRNAs were translated as efficiently as the host cell transcriptome, and sequestered up to 15% of the total ribosome occupancy. During cell culture, changes in recombinant mRNA translation were consistent with changes in transcription, demonstrating that transcript levels influence specific productivity. Using this information, we identified the unnecessary resistance marker NeoR to be a highly transcribed and translated gene. Through siRNA knock-down of NeoR, we improved the production- and growth capacity of the host cell. Thus, ribosomal profiling provides valuable insights into translation in CHO cells and can guide efforts to enhance protein production.
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172
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van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson BO, Lewis NE, Nizet V, Esko JD. Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion. mBio 2017; 8:e02128-16. [PMID: 28074024 PMCID: PMC5225314 DOI: 10.1128/mbio.02128-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/01/2016] [Indexed: 11/20/2022] Open
Abstract
To understand the role of glycosaminoglycans in bacterial cellular invasion, xylosyltransferase-deficient mutants of Chinese hamster ovary (CHO) cells were created using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (CRISPR-cas9) gene targeting. When these mutants were compared to the pgsA745 cell line, a CHO xylosyltransferase mutant generated previously using chemical mutagenesis, an unexpected result was obtained. Bacterial invasion of pgsA745 cells by group B Streptococcus (GBS), group A Streptococcus, and Staphylococcus aureus was markedly reduced compared to the invasion of wild-type cells, but newly generated CRISPR-cas9 mutants were only resistant to GBS. Invasion of pgsA745 cells was not restored by transfection with xylosyltransferase, suggesting that an additional mutation conferring panresistance to multiple bacteria was present in pgsA745 cells. Whole-genome sequencing and transcriptome sequencing (RNA-Seq) uncovered a deletion in the gene encoding the laminin subunit α2 (Lama2) that eliminated much of domain L4a. Silencing of the long Lama2 isoform in wild-type cells strongly reduced bacterial invasion, whereas transfection with human LAMA2 cDNA significantly enhanced invasion in pgsA745 cells. The addition of exogenous laminin-α2β1γ1/laminin-α2β2γ1 strongly increased bacterial invasion in CHO cells, as well as in human alveolar basal epithelial and human brain microvascular endothelial cells. Thus, the L4a domain in laminin α2 is important for cellular invasion by a number of bacterial pathogens. IMPORTANCE Pathogenic bacteria penetrate host cellular barriers by attachment to extracellular matrix molecules, such as proteoglycans, laminins, and collagens, leading to invasion of epithelial and endothelial cells. Here, we show that cellular invasion by the human pathogens group B Streptococcus, group A Streptococcus, and Staphylococcus aureus depends on a specific domain of the laminin α2 subunit. This finding may provide new leads for the molecular pathogenesis of these bacteria and the development of novel antimicrobial drugs.
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Affiliation(s)
- Xander M van Wijk
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Simon Döhrmann
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Björn M Hallström
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Royal Institute of Technology, Stockholm, Sweden
| | - Shangzhong Li
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, California, USA
| | - Bjørn G Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Brandon X Meng
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
| | - Karen K McKee
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Toin H van Kuppevelt
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Peter D Yurchenco
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Bernhard O Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, California, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, California, USA
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
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173
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Dahodwala H, Sharfstein ST. The 'Omics Revolution in CHO Biology: Roadmap to Improved CHO Productivity. Methods Mol Biol 2017; 1603:153-168. [PMID: 28493129 DOI: 10.1007/978-1-4939-6972-2_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Increased understanding of Chinese hamster ovary (CHO) cell physiology has been ushered in upon availability of the parental CHO-K1 cell line genome. Free and openly accessible sequence information has complemented transcriptomic and proteomic studies. The previous decade has also seen an increase in sensitivity and accuracy of proteomic methods due to technology development. In this genomic era, high-throughput screening methods, sophisticated informatic tools, and models continually drive major innovations in cell line development and process engineering. This review describes the various achievements in 'omics techniques and their application to improve recombinant protein expression from CHO cell lines.
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Affiliation(s)
- Hussain Dahodwala
- Vaccine production program (VPP), VRC/NIAID/NIH, Gaithersburg, MD, 20878, USA
- SUNY Polytechnic Institute, 257 Fuller Road, Albany, NY, 12203, USA
| | - Susan T Sharfstein
- Vaccine production program (VPP), VRC/NIAID/NIH, Gaithersburg, MD, 20878, USA.
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174
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A Bioinformatics Pipeline for the Identification of CHO Cell Differential Gene Expression from RNA-Seq Data. Methods Mol Biol 2017; 1603:169-186. [PMID: 28493130 DOI: 10.1007/978-1-4939-6972-2_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In recent years, the publication of genome sequences for the Chinese hamster and Chinese hamster ovary (CHO) cell lines has facilitated study of these biopharmaceutical cell factories with unprecedented resolution. Our understanding of the CHO cell transcriptome, in particular, has rapidly advanced through the application of next-generation sequencing (NGS) technology to characterize RNA expression (RNA-Seq). In this chapter, we present a computational pipeline for the analysis of CHO cell RNA-Seq data from the Illumina platform to identify differentially expressed genes. The example data and bioinformatics workflow required to run this analysis are freely available at www.cgcdb.org/rnaseq_analysis_protocol.html .
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175
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Hansen HG, Pristovšek N, Kildegaard HF, Lee GM. Improving the secretory capacity of Chinese hamster ovary cells by ectopic expression of effector genes: Lessons learned and future directions. Biotechnol Adv 2017; 35:64-76. [DOI: 10.1016/j.biotechadv.2016.11.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/12/2016] [Accepted: 11/28/2016] [Indexed: 12/12/2022]
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176
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Henry M, Coleman O, Clynes M, Meleady P. Phosphopeptide Enrichment and LC-MS/MS Analysis to Study the Phosphoproteome of Recombinant Chinese Hamster Ovary Cells. Methods Mol Biol 2017; 1603:195-208. [PMID: 28493132 DOI: 10.1007/978-1-4939-6972-2_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The reversible phosphorylation of proteins on serine, threonine, and tyrosine residues is one of the most important post-translational modifications that regulates many biological processes. The phosphoproteome has not been studied in any great detail in recombinant Chinese hamster ovary (CHO) cells to date despite phosphorylation playing a crucial role in regulating many molecular and cellular processes relevant to bioprocess phenotypes including, for example, transcription, translation, growth, apoptosis, and signal transduction. In this chapter, we provide a protocol for the phosphoproteomic analysis of Chinese hamster ovary cells using phosphopeptide enrichment with metal oxide affinity chromatography (MOAC) and immobilized metal affinity chromatography (IMAC) techniques, followed by site-specific identification of phosphorylated residues using LC-MS (MS2 and MS3) strategies.
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Affiliation(s)
- Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | - Orla Coleman
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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177
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Affiliation(s)
- Jennifer Pfizenmaier
- University of Stuttgart; Institute of Biochemical Engineering; Allmandring 31 70569 Stuttgart Germany
| | - Ralf Takors
- University of Stuttgart; Institute of Biochemical Engineering; Allmandring 31 70569 Stuttgart Germany
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178
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Hefzi H, Ang KS, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D, Martinez VS, Kyriakopoulos S, Jiménez NE, Zielinski DC, Quek LE, Wulff T, Arnsdorf J, Li S, Lee JS, Paglia G, Loira N, Spahn PN, Pedersen LE, Gutierrez JM, King ZA, Lund AM, Nagarajan H, Thomas A, Abdel-Haleem AM, Zanghellini J, Kildegaard HF, Voldborg BG, Gerdtzen ZP, Betenbaugh MJ, Palsson BO, Andersen MR, Nielsen LK, Borth N, Lee DY, Lewis NE. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst 2016; 3:434-443.e8. [PMID: 27883890 PMCID: PMC5132346 DOI: 10.1016/j.cels.2016.10.020] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/16/2016] [Accepted: 10/21/2016] [Indexed: 12/22/2022]
Abstract
Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell-line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show that the metabolic resources in CHO are more than three times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.
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Affiliation(s)
- Hooman Hefzi
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kok Siong Ang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore
| | - Michael Hanscho
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria
| | - Aarash Bordbar
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Ruckerbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore
| | - Camila A Orellana
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia
| | - Deniz Baycin-Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yingxiang Huang
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA
| | - Daniel Ley
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Veronica S Martinez
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia
| | - Sarantos Kyriakopoulos
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore
| | - Natalia E Jiménez
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lake-Ee Quek
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Johnny Arnsdorf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Shangzhong Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jae Seong Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Giuseppe Paglia
- Center for Systems Biology, University of Iceland, 101 Reykjavik, Iceland
| | - Nicolas Loira
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile
| | - Philipp N Spahn
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lasse E Pedersen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jahir M Gutierrez
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zachary A King
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anne Mathilde Lund
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Harish Nagarajan
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA
| | - Alex Thomas
- Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla 92093, CA, USA
| | - Alyaa M Abdel-Haleem
- Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Computational Bioscience Research Centre, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Juergen Zanghellini
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria
| | - Helene F Kildegaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Bjørn G Voldborg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ziomara P Gerdtzen
- Centre for Biotechnology and Bioengineering, Department of Chemical Engineering and Biotechnology, University of Chile, Santiago 8370456, Chile; MATHomics, Center for Mathematical Modeling; Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago 8370456, Chile
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD 4072, Australia
| | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology, 1190 Vienna, Austria.
| | - Dong-Yup Lee
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A(∗)STAR), 20 Biopolis Way, 06-01, Centros, Singapore 138668, Singapore.
| | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at the School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
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179
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Lee N, Shin J, Park JH, Lee GM, Cho S, Cho BK. Targeted Gene Deletion Using DNA-Free RNA-Guided Cas9 Nuclease Accelerates Adaptation of CHO Cells to Suspension Culture. ACS Synth Biol 2016; 5:1211-1219. [PMID: 26854539 DOI: 10.1021/acssynbio.5b00249] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chinese hamster ovary (CHO) cells are the preferred host for the production of a wide array of biopharmaceuticals. Thus, efficient and rational CHO cell line engineering methods have been in high demand to improve quality and productivity. Here, we provide a novel genome engineering platform for increasing desirable phenotypes of CHO cells based upon the integrative protocol of high-throughput RNA sequencing and DNA-free RNA-guided Cas9 (CRISPR associated protein9) nuclease-based genome editing. For commercial production of therapeutic proteins, CHO cells have been adapted for suspension culture in serum-free media, which is highly beneficial with respect to productivity and economics. To engineer CHO cells for rapid adaptation to a suspension culture, we exploited strand-specific RNA-seq to identify genes differentially expressed according to their adaptation trajectory in serum-free media. More than 180 million sequencing reads were generated and mapped to the currently available 109,152 scaffolds of the CHO-K1 genome. We identified significantly downregulated genes according to the adaptation trajectory and then verified their effects using the genome editing method. Growth-based screening and targeted amplicon sequencing revealed that the functional deletions of Igfbp4 and AqpI gene accelerate suspension adaptation of CHO-K1 cells. The availability of this strand-specific transcriptome sequencing and DNA-free RNA-guided Cas9 nuclease mediated genome editing facilitates the rational design of the CHO cell genome for efficient production of high quality therapeutic proteins.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - JongOh Shin
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Jin Hyoung Park
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, KAIST , Daejeon 305-701, Republic of Korea
- Intelligent Synthetic Biology Center, Daejeon 305-701, Republic of Korea
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180
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181
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Zucchelli S, Patrucco L, Persichetti F, Gustincich S, Cotella D. Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs. Comput Struct Biotechnol J 2016; 14:404-410. [PMID: 27872686 PMCID: PMC5107644 DOI: 10.1016/j.csbj.2016.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.
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Affiliation(s)
- Silvia Zucchelli
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Area of Neuroscience, SISSA, Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Neuroscience and Brain Technologies, Italian Institute of Technology (IIT), Genova, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
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182
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Mascarenhas JX, Korokhov N, Burger L, Kassim A, Tuter J, Miller D, Borgschulte T, George HJ, Chang A, Pintel DJ, Onions D, Kayser KJ. Genetic engineering of CHO cells for viral resistance to minute virus of mice. Biotechnol Bioeng 2016; 114:576-588. [PMID: 27642072 DOI: 10.1002/bit.26186] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/06/2016] [Accepted: 09/13/2016] [Indexed: 12/14/2022]
Abstract
Contamination by the parvovirus minute virus of mice (MVM) remains a challenge in Chinese hamster ovary (CHO) biopharmaceutical production processes. Although infrequent, infection of a bioreactor can be catastrophic for a manufacturer, can impact patient drug supply and safety, and can have regulatory implications. We evaluated engineering a CHO parental cell line (CHOZN® GS-/- ) to create a new host cell line that is resistant to MVM infection by modifying the major receptors used by the virus to enter cells. Attachment to a cell surface receptor is a key first step in the infection cycle for many viruses. While the exact functional receptor for MVM binding to CHO cell surface is unknown, sialic acid on the cell surface has been implicated. In this work, we used the zinc finger nuclease gene editing technology to validate the role of sialic acid on the cell surface in the binding and internalization of the MVM virus. Our approach was to systematically mutate genes involved in cell surface sialylation and then challenge each cell line for their ability to resist viral entry and propagation. To test the importance of sialylation, the following genes were knocked out: the CMP-sialic acid transporter, solute carrier family 35A1 (Slc35a1), the core 1-β-1,3-galactosyltransferase-1 specific chaperone (Cosmc), and mannosyl (α-1,3-)-glycoprotein β-1,2-N-acetylglucosaminyltransferase (Mgat1) as well as members of the sialyltransferase family. Slc35a1 is responsible for transporting sialic acid into the Golgi. Knocking out function of this gene in a cell results in asialylated glycan structures, thus eliminating the ability of MVM to bind to and enter the cell. The complete absence of sialic acid on the Slc35a1 knockout cell line led to complete resistance to MVM infection. The Cosmc and Mgat1 knockouts also show significant inhibition of infection likely due to their effect on decreasing cell surface sialic acid. Previously in vitro glycan analysis has been used to elucidate the precise sialic acid structures required for MVM binding and internalization. In this work, we performed the sequential knockout of various sialyltransferases that add terminal sialic acid to glycans with different linkage specificities. Cell lines with modifications of the various genes included in this study resulted in varying effects on MVM infection expanding on the knowledge of MVM receptors. MVM resistant host cell lines were also tested for the production of model recombinant proteins. Our data demonstrate that resistance against the MVM virus can be incorporated into CHO production cell lines, adding another level of defense against the devastating financial consequences of MVM infection without compromising recombinant protein yield or quality. Biotechnol. Bioeng. 2017;114: 576-588. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | | | - Lisa Burger
- University of Missouri School of Medicine, Columbia, Missouri
| | - Ademola Kassim
- Cell Sciences and Development, SAFC MilliporeSigma, Saint Louis, Missouri, 63103
| | - Jason Tuter
- Cell Sciences and Development, SAFC MilliporeSigma, Saint Louis, Missouri, 63103
| | - Daniel Miller
- Cell Sciences and Development, SAFC MilliporeSigma, Saint Louis, Missouri, 63103
| | - Trissa Borgschulte
- Cell Sciences and Development, SAFC MilliporeSigma, Saint Louis, Missouri, 63103
| | - Henry J George
- Cell Sciences and Development, SAFC MilliporeSigma, Saint Louis, Missouri, 63103
| | - Audrey Chang
- Bioreliance, MilliporeSigma, Rockville, Maryland
| | - David J Pintel
- University of Missouri School of Medicine, Columbia, Missouri
| | - David Onions
- Bioreliance, MilliporeSigma, Rockville, Maryland
| | - Kevin J Kayser
- Cell Sciences and Development, SAFC MilliporeSigma, Saint Louis, Missouri, 63103
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183
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Sharfstein ST. Omics insights into production-scale bioreactors. Biotechnol J 2016; 11:1124-5. [DOI: 10.1002/biot.201600338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 06/01/2016] [Accepted: 06/15/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Susan T. Sharfstein
- Colleges of Nanoscale Science and Engineering; SUNY Polytechnic Institute; 257 Fuller Road Albany NY 12203 USA
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184
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Abstract
Gene editing with all its own advantages in molecular biology applications has made easy manipulation of various production hosts with the discovery and implementation of modern gene editing tools such as Crispr (Clustered regularly interspaced short palindromic repeats), TALENs (Transcription activator-like effector nucleases) and ZFNs (Zinc finger nucleases). With the advent of these modern tools, it is now possible to manipulate the genome of industrial production hosts such as yeast and mammalian cells which allows developing a potential and cost effective recombinant therapeutic protein. These tools also allow single editing to multiple genes for knocking-in or knocking-out of a host genome quickly in an efficient manner. A recent study on "multiplexed" gene editing revolutionized the knock-out and knock-in events of yeast and CHO, mammalian cells genome for metabolic engineering as well as high, stable, and consistent expression of a transgene encoding complex therapeutic protein such as monoclonal antibody. The gene of interest can either be integrated or deleted at single or multiple loci depending on the strategy and production requirement. This review will give a gist of all the modern tools with a brief description and advances in genetic manipulation using three major tools being implemented for the modification of such hosts with the emphasis on the use of Crispr-Cas9 for the "multiplexing gene-editing approach" for genetic manipulation of yeast and CHO mammalian hosts that ultimately leads to a fast track product development with consistent, improved product yield, quality, and thus affordability for a population at large.
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Affiliation(s)
- Sanjeev K Gupta
- a Department of Microbiology, Enzyme Technology and Protein Bioinformatics Laboratory , Maharshi Dayanand University , Rohtak , Haryana , India.,b Advanced Biotech Lab (Centre for Research & Development), Ipca Laboratories Ltd , Kandivli, Mumbai , Maharashtra , India
| | - Pratyoosh Shukla
- a Department of Microbiology, Enzyme Technology and Protein Bioinformatics Laboratory , Maharshi Dayanand University , Rohtak , Haryana , India
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185
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Yamano N, Takahashi M, Ali Haghparast SM, Onitsuka M, Kumamoto T, Frank J, Omasa T. Increased recombinant protein production owing to expanded opportunities for vector integration in high chromosome number Chinese hamster ovary cells. J Biosci Bioeng 2016; 122:226-31. [DOI: 10.1016/j.jbiosc.2016.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/28/2015] [Accepted: 01/05/2016] [Indexed: 10/22/2022]
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186
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Popp O, Müller D, Didzus K, Paul W, Lipsmeier F, Kirchner F, Niklas J, Mauch K, Beaucamp N. A hybrid approach identifies metabolic signatures of high-producers for chinese hamster ovary clone selection and process optimization. Biotechnol Bioeng 2016; 113:2005-19. [DOI: 10.1002/bit.25958] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/01/2015] [Accepted: 02/14/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Oliver Popp
- Pharma Research and Early Development; Cell Culture Research, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Nonnenwald 2 D-82377 Penzberg Germany
| | - Dirk Müller
- Insilico Biotechnology AG; Stuttgart Germany
| | - Katharina Didzus
- Pharma Research and Early Development; Cell Culture Research, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Nonnenwald 2 D-82377 Penzberg Germany
| | - Wolfgang Paul
- Pharma Research and Early Development; Cell Culture Research, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Nonnenwald 2 D-82377 Penzberg Germany
| | - Florian Lipsmeier
- Pharma Research and Early Development, pRED Informatics, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Penzberg Germany
| | | | - Jens Niklas
- Insilico Biotechnology AG; Stuttgart Germany
| | - Klaus Mauch
- Insilico Biotechnology AG; Stuttgart Germany
| | - Nicola Beaucamp
- Pharma Research and Early Development; Cell Culture Research, Roche Innovation Center Penzberg; Roche Diagnostics GmbH; Nonnenwald 2 D-82377 Penzberg Germany
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187
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Vishwanathan N, Bandyopadhyay AA, Fu HY, Sharma M, Johnson KC, Mudge J, Ramaraj T, Onsongo G, Silverstein KAT, Jacob NM, Le H, Karypis G, Hu WS. Augmenting Chinese hamster genome assembly by identifying regions of high confidence. Biotechnol J 2016; 11:1151-7. [DOI: 10.1002/biot.201500455] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Nandita Vishwanathan
- Department of Chemical Engineering and Materials Science; University of Minnesota; Minneapolis MN USA
| | - Arpan A. Bandyopadhyay
- Department of Chemical Engineering and Materials Science; University of Minnesota; Minneapolis MN USA
| | - Hsu-Yuan Fu
- Department of Chemical Engineering and Materials Science; University of Minnesota; Minneapolis MN USA
| | - Mohit Sharma
- Department of Computer Science & Engineering; University of Minnesota; Minneapolis MN USA
| | - Kathryn C. Johnson
- Department of Chemical Engineering and Materials Science; University of Minnesota; Minneapolis MN USA
| | - Joann Mudge
- National Center for Genome Resources (NCGR); Santa Fe New Mexico USA
| | | | - Getiria Onsongo
- Minnesota Supercomputing Institute (MSI); University of Minnesota; Minneapolis MN USA
| | | | - Nitya M. Jacob
- Department of Chemical Engineering and Materials Science; University of Minnesota; Minneapolis MN USA
| | - Huong Le
- Department of Chemical Engineering and Materials Science; University of Minnesota; Minneapolis MN USA
| | - George Karypis
- Department of Computer Science & Engineering; University of Minnesota; Minneapolis MN USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science; University of Minnesota; Minneapolis MN USA
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188
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Gao Y, Ray S, Dai S, Ivanov AR, Abu-Absi NR, Lewis AM, Huang Z, Xing Z, Borys MC, Li ZJ, Karger BL. Combined metabolomics and proteomics reveals hypoxia as a cause of lower productivity on scale-up to a 5000-liter CHO bioprocess. Biotechnol J 2016; 11:1190-200. [DOI: 10.1002/biot.201600030] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/12/2016] [Accepted: 05/18/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Yuanwei Gao
- Barnett Institute and Department of Chemistry and Chemical Biology; Northeastern University; Boston MA USA
| | - Somak Ray
- Barnett Institute and Department of Chemistry and Chemical Biology; Northeastern University; Boston MA USA
| | - Shujia Dai
- Barnett Institute and Department of Chemistry and Chemical Biology; Northeastern University; Boston MA USA
| | - Alexander R. Ivanov
- Barnett Institute and Department of Chemistry and Chemical Biology; Northeastern University; Boston MA USA
| | - Nicholas R. Abu-Absi
- Biologics Development, Global Manufacturing and Supply; Bristol-Myers Squibb; 38 Jackson Road Devens MA USA
| | - Amanda M. Lewis
- Biologics Development, Global Manufacturing and Supply; Bristol-Myers Squibb; 38 Jackson Road Devens MA USA
| | - Zhuangrong Huang
- Biologics Development, Global Manufacturing and Supply; Bristol-Myers Squibb; 38 Jackson Road Devens MA USA
| | - Zizhuo Xing
- Biologics Development, Global Manufacturing and Supply; Bristol-Myers Squibb; 38 Jackson Road Devens MA USA
| | - Michael C. Borys
- Biologics Development, Global Manufacturing and Supply; Bristol-Myers Squibb; 38 Jackson Road Devens MA USA
| | - Zheng Jian Li
- Biologics Development, Global Manufacturing and Supply; Bristol-Myers Squibb; 38 Jackson Road Devens MA USA
| | - Barry L. Karger
- Barnett Institute and Department of Chemistry and Chemical Biology; Northeastern University; Boston MA USA
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189
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Multiscale approach predictions for biological outcomes in ion-beam cancer therapy. Sci Rep 2016; 6:27654. [PMID: 27297618 PMCID: PMC4906349 DOI: 10.1038/srep27654] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/26/2016] [Indexed: 11/25/2022] Open
Abstract
Ion-beam therapy provides advances in cancer treatment, offering the possibility of excellent dose localization and thus maximising cell-killing within the tumour. The full potential of such therapy can only be realised if the fundamental mechanisms leading to lethal cell damage under ion irradiation are well understood. The key question is whether it is possible to quantitatively predict macroscopic biological effects caused by ion radiation on the basis of physical and chemical effects related to the ion-medium interactions on a nanometre scale. We demonstrate that the phenomenon-based MultiScale Approach to the assessment of radiation damage with ions gives a positive answer to this question. We apply this approach to numerous experiments where survival curves were obtained for different cell lines and conditions. Contrary to other, in essence empirical methods for evaluation of macroscopic effects of ionising radiation, the MultiScale Approach predicts the biodamage based on the physical effects related to ionisation of the medium, transport of secondary particles, chemical interactions, thermo-mechanical pathways of biodamage, and heuristic biological criteria for cell survival. We anticipate this method to give great impetus to the practical improvement of ion-beam cancer therapy and the development of more efficient treatment protocols.
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190
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Ritter A, Rauschert T, Oertli M, Piehlmaier D, Mantas P, Kuntzelmann G, Lageyre N, Brannetti B, Voedisch B, Geisse S, Jostock T, Laux H. Disruption of the gene C12orf35
leads to increased productivities in recombinant CHO cell lines. Biotechnol Bioeng 2016; 113:2433-42. [DOI: 10.1002/bit.26009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/08/2016] [Accepted: 05/09/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Anett Ritter
- Novartis Institutes for BioMedical Research; Basel Switzerland
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | | | - Mevion Oertli
- Novartis Institutes for BioMedical Research; Basel Switzerland
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | - Daniel Piehlmaier
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | - Panagiotis Mantas
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | | | - Nadine Lageyre
- Novartis Institutes for BioMedical Research; Basel Switzerland
| | | | - Bernd Voedisch
- Novartis Institutes for BioMedical Research; Basel Switzerland
| | - Sabine Geisse
- Novartis Institutes for BioMedical Research; Basel Switzerland
| | - Thomas Jostock
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
| | - Holger Laux
- Novartis Pharma AG; Integrated Biologics Profiling Unit, Werk Klybeck Postfach CH-4002; Basel Switzerland
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191
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Priola JJ, Calzadilla N, Baumann M, Borth N, Tate CG, Betenbaugh MJ. High-throughput screening and selection of mammalian cells for enhanced protein production. Biotechnol J 2016; 11:853-65. [DOI: 10.1002/biot.201500579] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 02/09/2016] [Accepted: 05/17/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Joseph J. Priola
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore MD USA
| | - Nathan Calzadilla
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore MD USA
| | | | - Nicole Borth
- Department of Biotechnology; Universität für Bodenkultur; Vienna Austria
| | | | - Michael J. Betenbaugh
- Department of Chemical and Biomolecular Engineering; Johns Hopkins University; Baltimore MD USA
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192
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Feichtinger J, Hernández I, Fischer C, Hanscho M, Auer N, Hackl M, Jadhav V, Baumann M, Krempl PM, Schmidl C, Farlik M, Schuster M, Merkel A, Sommer A, Heath S, Rico D, Bock C, Thallinger GG, Borth N. Comprehensive genome and epigenome characterization of CHO cells in response to evolutionary pressures and over time. Biotechnol Bioeng 2016; 113:2241-53. [PMID: 27072894 PMCID: PMC5006888 DOI: 10.1002/bit.25990] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 03/15/2016] [Accepted: 04/07/2016] [Indexed: 01/03/2023]
Abstract
The most striking characteristic of CHO cells is their adaptability, which enables efficient production of proteins as well as growth under a variety of culture conditions, but also results in genomic and phenotypic instability. To investigate the relative contribution of genomic and epigenetic modifications towards phenotype evolution, comprehensive genome and epigenome data are presented for six related CHO cell lines, both in response to perturbations (different culture conditions and media as well as selection of a specific phenotype with increased transient productivity) and in steady state (prolonged time in culture under constant conditions). Clear transitions were observed in DNA‐methylation patterns upon each perturbation, while few changes occurred over time under constant conditions. Only minor DNA‐methylation changes were observed between exponential and stationary growth phase; however, throughout a batch culture the histone modification pattern underwent continuous adaptation. Variation in genome sequence between the six cell lines on the level of SNPs, InDels, and structural variants is high, both upon perturbation and under constant conditions over time. The here presented comprehensive resource may open the door to improved control and manipulation of gene expression during industrial bioprocesses based on epigenetic mechanisms. Biotechnol. Bioeng. 2016;113: 2241–2253. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Julia Feichtinger
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Inmaculada Hernández
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Christoph Fischer
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Michael Hanscho
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Norbert Auer
- University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria
| | - Matthias Hackl
- University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Martina Baumann
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Peter M Krempl
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Christian Schmidl
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Matthias Farlik
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | | | - Andreas Sommer
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Simon Heath
- Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Daniel Rico
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | - Gerhard G Thallinger
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria.,Graz University of Technology, Graz, Austria
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria. .,University of Natural Resources and Life Sciences Vienna, Muthgasse 18, Vienna, 1190, Austria.
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193
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Zhu G, Sun L, Albanetti T, Linkous T, Larkin C, Schoner R, McGivney JB, Dovichi NJ. Quantitative analysis of the supernatant from host and transfected CHO cells using iTRAQ 8-plex technique. Biotechnol Bioeng 2016; 113:2140-8. [DOI: 10.1002/bit.25991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/19/2016] [Accepted: 04/07/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Guijie Zhu
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame Indiana 46556
| | - Liangliang Sun
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame Indiana 46556
| | - Thomas Albanetti
- BioPharmaceutical Development MedImmune LLC; Gaithersburg Maryland
| | - Travis Linkous
- BioPharmaceutical Development MedImmune LLC; Gaithersburg Maryland
| | | | - Ronald Schoner
- BioPharmaceutical Development MedImmune LLC; Gaithersburg Maryland
| | | | - Norman J. Dovichi
- Department of Chemistry and Biochemistry; University of Notre Dame; Notre Dame Indiana 46556
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194
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Wright C, Groot J, Swahn S, McLaughlin H, Liu M, Xu C, Sun C, Zheng E, Estes S. Genetic mutation analysis at early stages of cell line development using next generation sequencing. Biotechnol Prog 2016; 32:813-7. [DOI: 10.1002/btpr.2263] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/08/2016] [Indexed: 11/09/2022]
Affiliation(s)
| | - Joost Groot
- Computational Biology and Genomics; Biogen; Cambridge MA
| | | | | | - Mei Liu
- Computational Biology and Genomics; Biogen; Cambridge MA
| | | | - Chao Sun
- Computational Biology and Genomics; Biogen; Cambridge MA
| | - Eric Zheng
- Computational Biology and Genomics; Biogen; Cambridge MA
| | - Scott Estes
- Cell Culture Development; Biogen; Cambridge MA
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195
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miRNA profiling of high, low and non-producing CHO cells during biphasic fed-batch cultivation reveals process relevant targets for host cell engineering. J Biotechnol 2016; 225:31-43. [PMID: 27002234 DOI: 10.1016/j.jbiotec.2016.03.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/11/2016] [Accepted: 03/17/2016] [Indexed: 01/01/2023]
Abstract
Fed-batch cultivation of recombinant Chinese hamster ovary (CHO) cell lines is one of the most widely used production modes for commercial manufacturing of recombinant protein therapeutics. Furthermore, fed-batch cultivations are often conducted as biphasic processes where the culture temperature is decreased to maximize volumetric product yields. However, it remains to be elucidated which intracellular regulatory elements actually control the observed pro-productive phenotypes. Recently, several studies have revealed microRNAs (miRNAs) to be important molecular switches of cell phenotypes. In this study, we analyzed miRNA profiles of two different recombinant CHO cell lines (high and low producer), and compared them to a non-producing CHO DG44 host cell line during fed-batch cultivation at 37°C versus a temperature shift to 30°C. Taking advantage of next-generation sequencing combined with cluster, correlation and differential expression analyses, we could identify 89 different miRNAs, which were differentially expressed in the different cell lines and cultivation phases. Functional validation experiments using 19 validated target miRNAs confirmed that these miRNAs indeed induced changes in process relevant phenotypes. Furthermore, computational miRNA target prediction combined with functional clustering identified putative target genes and cellular pathways, which might be regulated by these miRNAs. This study systematically identified novel target miRNAs during different phases and conditions of a biphasic fed-batch production process and functionally evaluated their potential for host cell engineering.
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196
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Bedoya-López A, Estrada K, Sanchez-Flores A, Ramírez OT, Altamirano C, Segovia L, Miranda-Ríos J, Trujillo-Roldán MA, Valdez-Cruz NA. Effect of Temperature Downshift on the Transcriptomic Responses of Chinese Hamster Ovary Cells Using Recombinant Human Tissue Plasminogen Activator Production Culture. PLoS One 2016; 11:e0151529. [PMID: 26991106 PMCID: PMC4798216 DOI: 10.1371/journal.pone.0151529] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/28/2016] [Indexed: 12/30/2022] Open
Abstract
Recombinant proteins are widely used as biopharmaceuticals, but their production by mammalian cell culture is expensive. Hence, improvement of bioprocess productivity is greatly needed. A temperature downshift (TDS) from 37°C to 28–34°C is an effective strategy to expand the productive life period of cells and increase their productivity (qp). Here, TDS in Chinese hamster ovary (CHO) cell cultures, initially grown at 37°C and switched to 30°C during the exponential growth phase, resulted in a 1.6-fold increase in the qp of recombinant human tissue plasminogen activator (rh-tPA). The transcriptomic response using next-generation sequencing (NGS) was assessed to characterize the cellular behavior associated with TDS. A total of 416 (q > 0.8) and 3,472 (q > 0.9) differentially expressed transcripts, with more than a 1.6-fold change at 24 and 48 h post TDS, respectively, were observed in cultures with TDS compared to those at constant 37°C. In agreement with the extended cell survival resulting from TDS, transcripts related to cell growth arrest that controlled cell proliferation without the activation of the DNA damage response, were differentially expressed. Most upregulated genes were related to energy metabolism in mitochondria, mitochondrial biogenesis, central metabolism, and avoidance of apoptotic cell death. The gene coding for rh-tPA was not differentially expressed, but fluctuations were detected in the transcripts encoding proteins involved in the secretory machinery, particularly in glycosylation. Through NGS the dynamic processes caused by TDS were assessed in this biological system.
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Affiliation(s)
- Andrea Bedoya-López
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Karel Estrada
- Unidad Universitaria de Apoyo Bioinformático, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor. México
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Apoyo Bioinformático, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor. México
| | - Octavio T. Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor. México
| | - Claudia Altamirano
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Lorenzo Segovia
- Departamento de Ingeniería Celular y Biocatálisis. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor. México
| | - Juan Miranda-Ríos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Mauricio A. Trujillo-Roldán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Norma A. Valdez-Cruz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
- * E-mail:
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197
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A signature of 12 microRNAs is robustly associated with growth rate in a variety of CHO cell lines. J Biotechnol 2016; 235:150-61. [PMID: 26993211 DOI: 10.1016/j.jbiotec.2016.03.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 12/25/2022]
Abstract
As Chinese Hamster Ovary (CHO) cells are the cell line of choice for the production of human-like recombinant proteins, there is interest in genetic optimization of host cell lines to overcome certain limitations in their growth rate and protein secretion. At the same time, a detailed understanding of these processes could be used to advantage by identification of marker transcripts that characterize states of performance. In this context, microRNAs (miRNAs) that exhibit a robust correlation to the growth rate of CHO cells were determined by analyzing miRNA expression profiles in a comprehensive collection of 46 samples including CHO-K1, CHO-S and CHO-DUKXB11, which were adapted to various culture conditions, and analyzed in different growth stages using microarrays. By applying Spearman or Pearson correlation coefficient criteria of>|0.6|, miRNAs with high correlation to the overall growth, or growth rates observed in exponential, serum-free, and serum-free exponential phase were identified. An overlap of twelve miRNAs common for all sample sets was revealed, with nine positively and three negatively correlating miRNAs. The here identified panel of miRNAs can help to understand growth regulation in CHO cells and contains putative engineering targets as well as biomarkers for cell lines with advantageous growth characteristics.
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198
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Chen C, Le H, Goudar CT. Integration of systems biology in cell line and process development for biopharmaceutical manufacturing. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2015.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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199
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Veith N, Ziehr H, MacLeod RAF, Reamon-Buettner SM. Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines. BMC Biotechnol 2016; 16:6. [PMID: 26800878 PMCID: PMC4722726 DOI: 10.1186/s12896-016-0238-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/15/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Recombinant cell lines developed for therapeutic antibody production often suffer instability or lose recombinant protein expression during long-term culture. Heterogeneous gene expression among cell line subclones may result from epigenetic modifications of DNA or histones, the protein component of chromatin. We thus investigated in such cell lines, DNA methylation and the chromatin environment along the human eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) promoter in an antibody protein-expression vector which was integrated into the Chinese hamster ovary (CHO) cell line genome. RESULTS We analyzed four PT1-CHO cell lines which exhibited losses of protein expression at advanced passage number (>P35) growing in adherent conditions and in culture medium with 10 % FCS. These cell lines exhibited different integration sites and transgene copy numbers as determined by fluorescence in situ hybridization (FISH) and quantitative PCR (qPCR), respectively. By qRT-PCR, we analyzed the recombinant mRNA expression and correlated it with DNA methylation and with results from various approaches interrogating the chromatin landscape along the EEF1A1 promoter region. Each PT1-CHO cell line displayed specific epigenetic signatures or chromatin marks correlating with recombinant mRNA expression. The cell line with the lowest recombinant mRNA expression (PT1-1) was characterized by the highest nucleosome occupancy and displayed the lowest enrichment for histone marks associated with active transcription. In contrast, the cell line with the highest recombinant mRNA expression (PT1-55) exhibited the highest numbers of formaldehyde-assisted isolation of regulatory elements (FAIRE)-enriched regions, and was marked by enrichment for histone modifications H3K9ac and H3K9me3. Another cell line with the second highest recombinant mRNA transcription and the most stable protein expression (PT1-7) had the highest enrichments of the histone variants H3.3 and H2A.Z, and the histone modification H3K9ac. A further cell line (PT1-30) scored the highest enrichments for the bivalent marks H3K4me3 and H3K27me3. Finally, DNA methylation made a contribution, but only in the culture medium with reduced FCS or in a different expression vector. CONCLUSIONS Our results suggest that the chromatin state along the EEF1A1 promoter region can help predict recombinant mRNA expression, and thus may assist in selecting desirable clones during cell line development for protein production.
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Affiliation(s)
- Nathalie Veith
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Holger Ziehr
- Pharmaceutical Biotechnology, Fraunhofer Institute for Toxicology and Experimental Medicine, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
| | - Roderick A F MacLeod
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124, Braunschweig, Germany.
| | - Stella Marie Reamon-Buettner
- Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs Strasse 1, 30625, Hannover, Germany.
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200
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Improving expression of recombinant human IGF-1 using IGF-1R knockout CHO cell lines. Biotechnol Bioeng 2016; 113:1094-101. [DOI: 10.1002/bit.25877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/11/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022]
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