Epigenomic features revealed by ATAC-seq impact transgene expression in CHO cells.
ATAC-seq
CHO
CRISPR/Cas9
super-enhancers
Journal
Biotechnology and bioengineering
ISSN: 1097-0290
Titre abrégé: Biotechnol Bioeng
Pays: United States
ID NLM: 7502021
Informations de publication
Date de publication:
05 2021
05 2021
Historique:
revised:
14
01
2021
received:
12
10
2020
accepted:
25
01
2021
pubmed:
2
2
2021
medline:
29
3
2022
entrez:
1
2
2021
Statut:
ppublish
Résumé
Different regions of a mammalian genome have different accessibilities to transcriptional machinery. The integration site of a transgene affects how actively it is transcribed. Highly accessible genomic regions called super-enhancers have been recently described as strong regulatory elements that shape cell identity. Super-enhancers have been identified in Chinese hamster ovary (CHO) cells using the Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq). Genes near super-enhancer regions had high transcript levels and were enriched for oncogenic signaling and proliferation functions, consistent with an immortalized phenotype. Inaccessible regions in the genome with low ATAC signal also had low transcriptional activity. Genes in inaccessible regions were enriched for remote tissue functions such as taste, smell, and neuronal activation. A lentiviral reporter integration assay showed integration into super-enhancer regions conferred higher reporter expression than insertion into inaccessible regions. Targeted integration of an IgG vector into the Plec super-enhancer region yielded clones that expressed the immunoglobulin light chain gene mostly in the top 20% of all transcripts with the majority in the top 5%. The results suggest the epigenomic landscape of CHO cells can guide the selection of integration sites in the development of cell lines for therapeutic protein production.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1851-1861Informations de copyright
© 2021 Wiley Periodicals LLC.
Références
Bandyopadhyay, A. A., O'Brien, S. A., Zhao, L., Fu, H. Y., Vishwanathan, N., & Hu, W. S. (2019). Recurring genomic structural variation leads to clonal instability and loss of productivity. Biotechnology and Bioengineering, 116(1), 41-53. https://doi.org/10.1002/bit.26823
Barnes, L. M., Bentley, C. M., & Dickson, A. J. (2003). Stability of protein production from recombinant mammalian cells. Biotechnology and Bioengineering, 81(6), 631-639. https://doi.org/10.1002/bit.10517
Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008). High-resolution mapping and characterization of open chromatin across the genome. Cell, 132(2), 311-322. https://doi.org/10.1016/j.cell.2007.12.014
Buenrostro, J. D., Wu, B., Chang, H. Y., & Greenleaf, W. J. (2015). ATAC-seq: A method for assaying chromatin accessibility genome-wide. Current Protocols in Molecular Biology, 109, 21.29.1-21.29.9 https://doi.org/10.1002/0471142727.mb2129s109
Carver, J., Ng, D., Zhou, M., Ko, P., Zhan, D., Yim, M., & Hu, Z. (2020). Maximizing antibody production in a targeted integration host by optimization of subunit gene dosage and position. Biotechnology Progress, e2967. https://doi.org/10.1002/btpr.2967
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., & Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819-823.
D'Alessio, A. C., Fan, Z. P., Wert, K. J., Baranov, P., Cohen, M. A., Saini, J. S., Cohick, E., Charniga, C., Dadon, D., Hannett, N. M., Young, M. J., Temple, S., Jaenisch, R., Lee, T. I., & Young, R. A. (2015). A systematic approach to identify candidate transcription factors that control cell identity. Stem Cell Reports, 5(5), 763-775. https://doi.org/10.1016/j.stemcr.2015.09.016
Filion, G. J., van Bemmel, J. G., Braunschweig, U., Talhout, W., Kind, J., Ward, L. D., Brugman, W., de Castro, I. J., Kerkhoven, R. M., Bussemaker, H. J., & van Steensel, B. (2010). Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell, 143(2), 212-224. https://doi.org/10.1016/j.cell.2010.09.009
Hoffman, M. M., Ernst, J., Wilder, S. P., Kundaje, A., Harris, R. S., Libbrecht, M., Giardine, B., Ellenbogen, P. M., Bilmes, J. A., Birney, E., Hardison, R. C., Dunham, I., Kellis, M., & Noble, W. S. (2013). Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Research, 41(2), 827-841. https://doi.org/10.1093/nar/gks1284
Huang, Y., Li, Y., Wang, Y. G., Gu, X., Wang, Y., & Shen, B. F. (2007). An efficient and targeted gene integration system for high-level antibody expression. Journal of Immunological Methods, 322(1-2), 28-39. https://doi.org/10.1016/j.jim.2007.01.022
Inniss, M. C., Bandara, K., Jusiak, B., Lu, T. K., Weiss, R., Wroblewska, L., & Zhang, L. (2017). A novel Bxb1 integrase RMCE system for high fidelity site-specific integration of mAb expression cassette in CHO Cells. Biotechnology and Bioengineering, 114(8), 1837-1846. https://doi.org/10.1002/bit.26268
Kim, M., O'Callaghan, P. M., Droms, K. A., & James, D. C. (2011). A mechanistic understanding of production instability in CHO cell lines expressing recombinant monoclonal antibodies. Biotechnology and Bioengineering, 108(10), 2434-2446. https://doi.org/10.1002/bit.23189
Kim, S. J., & Lee, G. M. (1999). Cytogenetic analysis of chimeric antibody-producing CHO cells in the course of dihydrofolate reductase-mediated gene amplification and their stability in the absence of selective pressure. Biotechnology and Bioengineering, 64(6), 741-749. https://doi.org/10.1002/(sici)1097-0290(19990920)64:6%3C741::Aid-bit14%3E3.0.Co;2-x
Kingston, R. E., Kaufman, R. J., Bebbington, C. R., & Rolfe, M. R. (2002). Amplification using CHO cell expression vectors. Current Protocols in Molecular Biology, 60(1), 16.23.11-16.23.13 https://doi.org/10.1002/0471142727.mb1623s60
Kito, M., Itami, S., Fukano, Y., Yamana, K., & Shibui, T. (2002). Construction of engineered CHO strains for high-level production of recombinant proteins. Applied Microbiology and Biotechnology, 60(4), 442-448. https://doi.org/10.1007/s00253-002-1134-1
Lee, J. S., Kallehauge, T. B., Pedersen, L. E., & Kildegaard, H. F. (2015). Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway. Scientific Reports, 5, 8572. https://doi.org/10.1038/srep08572
Lin, C. Y., Erkek, S., Tong, Y., Yin, L., Federation, A. J., Zapatka, M., Haldipur, P., Kawauchi, D., Risch, T., Warnatz, H. J., Worst, B. C., Ju, B., Orr, B. A., Zeid, R., Polaski, D. R., Segura-Wang, M., Waszak, S. M., Jones, D. T. W., Kool, M., … Northcott, P. A. (2016). Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature, 530(7588), 57-62. https://doi.org/10.1038/nature16546
Lovén, J., Hoke, H. A., Lin, C. Y., Lau, A., Orlando, D. A., Vakoc, C. R., Bradner, J. E., Lee, T. I., & Young, R. A. (2013). Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell, 153(2), 320-334. https://doi.org/10.1016/j.cell.2013.03.036
Moritz, B., Becker, P. B., & Gopfert, U. (2015). CMV promoter mutants with a reduced propensity to productivity loss in CHO cells. Scientific Reports, 5, 16952. https://doi.org/10.1038/srep16952
Nissom, P. M., Sanny, A., Kok, Y. J., Hiang, Y. T., Chuah, S. H., Shing, T. K., Lee, Y. Y., Wong, K. T. K., Hu, W., Sim, M. Y. G., & Philp, R. (2006). Transcriptome and proteome profiling to understanding the biology of high productivity CHO cells. Molecular Biotechnology, 34(2), 125-140. https://doi.org/10.1385/MB:34:2:125
Northcott, P. A., Lee, C., Zichner, T., Stütz, A. M., Erkek, S., Kawauchi, D., Shih, D. J. H., Hovestadt, V., Zapatka, M., Sturm, D., Jones, D. T. W., Kool, M., Remke, M., Cavalli, F. M. G., Zuyderduyn, S., Bader, G. D., VandenBerg, S., Esparza, L. A., Ryzhova, M., … Pfister, S. M. (2014). Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature, 511(7510), 428-434. https://doi.org/10.1038/nature13379
O'Brien, S. A., Lee, K., Fu, H. Y., Lee, Z., Le, T. S., Stach, C. S., McCann, M. G., Zhang, A. Q., Smanski, M. J., Somia, N. V., & Hu, W. S. (2018). Single copy transgene integration in a transcriptionally active site for recombinant protein synthesis. Biotechnology Journal, 13(10), e1800226. https://doi.org/10.1002/biot.201800226
O'Brien, S. A., Ojha, J., Wu, P., & Hu, W. S. (2020). Multiplexed clonality verification of cell lines for protein biologic production. Biotechnology Progress, 36(4), e2978. https://doi.org/10.1002/btpr.2978
Pei, H., Fu, H. Y., Hirai, H., Cho, D. S., O'Brien, T. D., Dutton, J., Verfaillie, C. M., & Hu, W. S. (2017). Generation of induced pluripotent stem cells from Chinese hamster embryonic fibroblasts. Stem Cell Research, 21, 132-136. https://doi.org/10.1016/j.scr.2017.04.010
Peng, Y., & Zhang, Y. (2018). Enhancer and super-enhancer: Positive regulators in gene transcription. Animal Models and Experimental Medicine, 1(3), 169-179. https://doi.org/10.1002/ame2.12032
Perry, M. W., Boettiger, A. N., & Levine, M. (2011). Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proceedings of the National Academy of Sciences of the United States of America, 108(33), 13570-13575. https://doi.org/10.1073/pnas.1109873108
Ronda, C., Pedersen, L. E., Hansen, H. G., Kallehauge, T. B., Betenbaugh, M. J., Nielsen, A. T., & Kildegaard, H. F. (2014). Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool. Biotechnology and Bioengineering, 111(8), 1604-1616. https://doi.org/10.1002/bit.25233
Semenkovich, N. P., Planer, J. D., Ahern, P. P., Griffin, N. W., Lin, C. Y., & Gordon, J. I. (2016). Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes. Proceedings of the National Academy of Sciences of the United States of America, 113(51), 14805-14810. https://doi.org/10.1073/pnas.1617793113
Sengupta, S., & George, R. E. (2017). Super-enhancer-driven transcriptional dependencies in cancer. Trends in Cancer, 3(4), 269-281. https://doi.org/10.1016/j.trecan.2017.03.006
Seth, G., Charaniya, S., Wlaschin, K. F., & Hu, W. S. (2007). In pursuit of a super producer-alternative paths to high producing recombinant mammalian cells. Current Opinion in Biotechnology, 18(6), 557-564. https://doi.org/10.1016/j.copbio.2007.10.012
Thandapani, P. (2019). Super-enhancers in cancer. Pharmacology and Therapeutics, 199, 129-138. https://doi.org/10.1016/j.pharmthera.2019.02.014
Vishwanathan, N., Bandyopadhyay, A., Fu, H. Y., Johnson, K. C., Springer, N. M., & Hu, W. S. (2017). A comparative genomic hybridization approach to study gene copy number variations among Chinese hamster cell lines. Biotechnology and Bioengineering, 114(8), 1903-1908. https://doi.org/10.1002/bit.26311
Vishwanathan, N., Bandyopadhyay, A. A., Fu, H. Y., Sharma, M., Johnson, K. C., Mudge, J., Ramaraj, T., Onsongo, G., Silverstein, K. A. T., Jacob, N. M., Le, H., Karypis, G., & Hu, W. S. (2016). Augmenting Chinese hamster genome assembly by identifying regions of high confidence. Biotechnology Journal, 11(9), 1151-1157. https://doi.org/10.1002/biot.201500455
Vishwanathan, N., Yongky, A., Johnson, K. C., Fu, H. Y., Jacob, N. M., Le, H., Yusufi, F. N. K., Lee, D. Y., & Hu, W. S. (2015). Global insights into the Chinese hamster and CHO cell transcriptomes. Biotechnology and Bioengineering, 112(5), 965-976. https://doi.org/10.1002/bit.25513
Walker, B. A., Wardell, C. P., Brioli, A., Boyle, E., Kaiser, M. F., Begum, D. B., Dahir, N. B., Johnson, D. C., Ross, F. M., Davies, F. E., & Morgan, G. J. (2014). Translocations at 8q24 juxtapose MYC with genes that harbor superenhancers resulting in overexpression and poor prognosis in myeloma patients. Blood Cancer Journal, 4, e191. https://doi.org/10.1038/bcj.2014.13
Wallrath, L. L., & Elgin, S. C. (1995). Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes and Development, 9(10), 1263-1277. https://doi.org/10.1101/gad.9.10.1263
Wang, Y., Zhang, T., Kwiatkowski, N., Abraham, B. J., Lee, T. I., Xie, S., Yuzugullu, H., Von, T., Li, H., Lin, Z., Stover, D. G., Lim, E., Wang, Z. C., Iglehart, J. D., Young, R. A., Gray, N. S., & Zhao, J. J. (2015). CDK7-dependent transcriptional addiction in triple-negative breast cancer. Cell, 163(1), 174-186. https://doi.org/10.1016/j.cell.2015.08.063
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013). Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153(2), 307-319. https://doi.org/10.1016/j.cell.2013.03.035
Wurm, F., & Wurm, M. (2017). Cloning of CHO cells, productivity and genetic stability-A discussion. Processes, 5(4), 20. https://doi.org/10.3390/pr5020020
Xu, X., Nagarajan, H., Lewis, N. E., Pan, S., Cai, Z., Liu, X., Chen, W., Xie, M., Wang, W., Hammond, S., Andersen, M. R., Neff, N., Passarelli, B., Koh, W., Fan, H. C., Wang, J., Gui, Y., Lee, K. H., Betenbaugh, M. J., & Wang, J. (2011). The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotechnology, 29(8), 735-741. https://doi.org/10.1038/nbt.1932
Zhang, L., Inniss, M. C., Han, S., Moffat, M., Jones, H., Zhang, B., Cox, W. L., Rance, J. R., & Young, R. J. (2015). Recombinase-mediated cassette exchange (RMCE) for monoclonal antibody expression in the commercially relevant CHOK1SV cell line. Biotechnology Progress, 31(6), 1645-1656. https://doi.org/10.1002/btpr.2175