Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome
Open accessAbstract
Chinese hamster ovary (CHO) cells, first isolated in 1957, are the preferred production host for many therapeutic proteins. Although genetic heterogeneity among CHO cell lines has been well documented, a systematic, nucleotide-resolution characterization of their genotypic differences has been stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages. This analysis identified hamster genes missing in different CHO cell lines, and detected >3.7 million single-nucleotide polymorphisms (SNPs), 551,240 indels and 7,063 copy number variations. Many mutations are located in genes with functions relevant to bioprocessing, such as apoptosis. The details of this genetic diversity highlight the value of the hamster genome as the reference upon which CHO cells can be studied and engineered for protein production.
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The publication of the CHO-K1 genome sequence in 2011, followed by the publication of two Chinese hamster and six CHO cell line genomes in 2013, bring new opportunities in developing and engineering CHO cells for improved glycoprotein production.
“The publication of the CHO-K1 genome sequence in 2011, followed by the publication of two Chinese hamster and six CHO cell line genomes in 2013, bring new opportunities in developing and engineering CHO cells for improved glycoprotein production (Xu et al., 2011;Brinkrolf et al., 2013;Lewis et al., 2013).”
From Therapeutic glycoprotein production in mammalian cells (2017) · cites this paper as Lewis et al., 2013
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556 · see citing works
Initial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187 · see citing works
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · see citing works
Self-citationA comprehensive catalogue of somatic mutations from a human cancer genome
Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M.-L., Ordóñez, G. R., Bignell, G. R., et al. (2010) · Nature · doi:10.1038/nature08658 · Cited by 1,696 · see citing works
mTOR and cancer: insights into a complex relationship
Sabatini, D. M. (2006) · Nature Reviews Cancer · doi:10.1038/nrc1974 · Cited by 1,322 · see citing works
Laurent, L. C., Ulitsky, I., Slavin, I., Tran, H., Schork, A., Morey, R., Lynch, C., Harness, J. V., Lee, S., Barrero, M. J., et al. (2011) · Cell stem cell · doi:10.1016/j.stem.2010.12.003 · Cited by 890 · see citing works
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line
Xu, X., Nagarajan, H., Lewis, N. E., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1932 · Cited by 785 · see citing works
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Research works printed but not linked: 2
- Kildegaard, H.F., Baycin-Hizal, D., Lewis, N.E. & Betenbaugh, M.J. The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology. Curr. Opin. Biotechnol. doi:10.1016/j.copbio.2013.02.007 (20 March 2013). · DOI · Paper page
- Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W. & Haussler, D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. USA 100, 11484-11489 (2003).
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Self-citationStolfa, G., Smonskey, M. T., Boniface, R., Hachmann, A., Gulde, P., Joshi, A. D., Pierce, A. P., Jacobia, S. J., & Campbell, A. (2018) · Biotechnology Journal · doi:10.1002/biot.201700227 · Cited by 97 · see citing works
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Yang, W. C., Lu, J., Nguyen, N. B., Zhang, A., Healy, N. V., Kshirsagar, R., Ryll, T., & Huang, Y.-M. (2014) · Molecular Biotechnology · doi:10.1007/s12033-013-9725-x · Cited by 89 · see citing works
Gao, Y., Ray, S., Dai, S., Ivanov, A. R., Abu‐Absi, N. R., Lewis, A. M., Huang, Z., Xing, Z., Borys, M. C., Li, Z. J., et al. (2016) · Biotechnology Journal · doi:10.1002/biot.201600030 · Cited by 76 · see citing works
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MacDonald, M. A., Nöbel, M., Roche Recinos, D., Martínez, V. S., Schulz, B. L., Howard, C. B., Baker, K., Shave, E., Lee, Y. Y., Marcellin, E., et al. (2022) · Critical Reviews in Biotechnology · doi:10.1080/07388551.2021.1998821 · Cited by 55 · see citing works
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- Authors
- Lewis, N. E., Liu, X., Li, Y., Nagarajan, H., Yerganian, G., O'Brien, E., Bordbar, A., Roth, A. M., Rosenbloom, J., Bian, C., Xie, M., Chen, W., Li, N., Baycin-Hizal, D., Latif, H., Forster, J., Betenbaugh, M. J., Famili, I., Xu, X., Wang, J., & Palsson, B. O.
- Affiliations
- Qualcomm (United States) (US)
- BGI Group (China) (CN)
- Brandeis University (US)
- Johns Hopkins University (US)
- Corresponding author
- Wang, Jun
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2013-07-21
- Volume
- 31
- Issue
- 8
- Pages
- 759-765
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2127173397
- Cited by
- 380
- References
- 8
- Citations by year
- 2026: 11 · 2025: 15 · 2024: 13 · 2023: 13 · 2022: 21 · 2021: 36 · 2020: 23 · 2019: 27 · 2018: 50 · 2017: 35 · 2016: 30 · 2015: 55 · 2014: 41 · 2013: 7 · 2012: 1
- FWCI
- 19.87
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Biotechnology (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
- Funders
- Novo Nordisk Fonden (NNF10CC1016517)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Viral Infectious Diseases and Gene Expression in Insects
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Animal Genetics and Reproduction
- Keywords
- CHO cells, Chinese hamster, draft genome sequence, single nucleotide polymorphisms, copy number variation, indels, CHO-K1 cells, apoptosis-related genes, bioprocessing, therapeutic protein production
- MeSH terms
- Animals, Base Sequence, Chromosome Mapping, Cricetulus, Female, Cricetinae, Humans, Molecular Sequence Data, Genetic Variation, CHO Cells, Genome, Sequence Analysis, DNA
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