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Kim D, Kim SH, Yoon C, Lee GM. Genome-wide CRISPR/Cas9 knockout screening to mitigate cell growth inhibition induced by histone deacetylase inhibitors in recombinant CHO cells. Biotechnol Bioeng 2024; 121:931-941. [PMID: 38013500 DOI: 10.1002/bit.28611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/07/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
Histone deacetylase inhibitors (iHDACs) have been extensively studied as enhancers of therapeutic protein production in recombinant Chinese hamster ovary (CHO) (rCHO) cell cultures. However, the addition of iHDACs reduces the viable cell concentration (VCC) in rCHO cell cultures, thereby reducing their potential to enhance therapeutic protein production. To mitigate the negative effects of iHDACs on VCC, screening using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-based single-gene knockout (KO) library in rCHO cells was performed in the presence of CI994, a member of iHDACs, and 10 potential KO genes that enhanced the VCC of CI994-treated rCHO cells were identified. Among these, Bcor was validated as a promising KO target that improved VCC without negatively affecting the specific productivity in the presence of CI994. Bcor KO increased the VCC and therapeutic protein concentrations in both batch and fed-batch cultures in the presence of CI994. Taken together, these findings highlight the potential of the whole-genome CRISPR/Cas9-based single-gene KO cell library to identify KO target genes for the development of iHDAC-resistant rCHO cells for enhanced therapeutic protein production.
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Affiliation(s)
- Dongil Kim
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Su Hyun Kim
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Chansik Yoon
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
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Kim TH, Song Z, Jung J, Sung JS, Kang MJ, Shim WB, Lee M, Pyun JC. Functionalized Parylene Films for Enhancement of Antibody Production by Hybridoma Cells. ACS Appl Bio Mater 2023; 6:3726-3738. [PMID: 37647153 DOI: 10.1021/acsabm.3c00417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In this study, the influence of microenvironments on antibody production of hybridoma cells was analyzed using six types of functionalized parylene films, parylene-N and parylene-C (before and after UV radiation), parylene-AM, and parylene-H, and using polystyrene as a negative control. Hybridoma cells were cultured on modified parylene films that produced a monoclonal antibody against the well-known fungal toxin ochratoxin-A. Surface properties were analyzed for each parylene film, such as roughness, chemical functional groups, and hydrophilicity. The proliferation rate of the hybridoma cells was observed for each parylene film by counting the number of adherent cells, and the total amount of produced antibodies from different parylene films was estimated using indirect ELISA. In comparison with the polystyrene, the antibody-production by parylene-H and parylene-AM was estimated to be observed to be as high as 210-244% after the culture of 24 h. These results indicate that the chemical functional groups of the culture plate could influence antibody production. To analyze the influence of the microenvironments of the modified parylene films, we performed cell cycle analysis to estimate the ratio of the G0/G1, S, and G2/M phases of the hybridoma cells on each parylene film. From the normalized proportion of phases of the cell cycle, the difference in antibody production from different surfaces was considered to result from the difference in the proliferation rate of hybridoma cells, which occurred from the different physical and chemical properties of the parylene films. Finally, protein expression was analyzed using an mRNA array to determine the effect of parylene films on protein expression in hybridoma cells. The expression of three antibody production-related genes (CD40, Sox4, and RelB) was analyzed in hybridoma cells cultured on modified parylene films.
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Affiliation(s)
- Tae-Hun Kim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Zhiquan Song
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Jaeyong Jung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Jeong-Soo Sung
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, South Korea
| | - Min-Jung Kang
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea
| | - Won-Bo Shim
- Department of Food Science and Technology & Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Gyeongnam 52828, South Korea
| | - Misu Lee
- Division of Life Sciences, College of Life Science and Bioengineering and △Institute for New Drug Development, College of Life Science and Bioengineering, Incheon National University, Incheon 22012, South Korea
| | - Jae-Chul Pyun
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-Ro, Seodaemun-gu, Seoul 03722, South Korea
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Kim D, Yoon C, Lee GM. Small molecule epigenetic modulators for enhancing recombinant antibody production in CHO cell cultures. Biotechnol Bioeng 2021; 119:820-831. [PMID: 34961935 DOI: 10.1002/bit.28013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 11/07/2022]
Abstract
Small molecule epigenetic modulators that modify epigenetic states in cells are useful tools for regulating gene expression by inducing chromatin remodeling. To identify small molecule epigenetic modulators that enhance recombinant protein expression in CHO cells, we examined eight histone deacetylase inhibitors (iHDACs) and six DNA methyltransferase inhibitors as chemical additives in recombinant CHO (rCHO) cell cultures. Among these, a benzamide-based iHDAC, CI994, was the most effective in increasing monoclonal antibody (mAb) production. Despite suppressing cell growth, the addition of CI994 to mAb-expressing GSR cell cultures at 10 μM resulted in a 2.3-fold increase in maximum mAb concentration due to a 3.0-fold increase in specific mAb productivity (q mAb ). CI994 increased mAb mRNA levels and histone H3 acetylation in GSR cells, and ChIP-qPCR analysis revealed that CI994 significantly increased the histone H3 acetylation level at the CMV promoter driving mAb gene expression, indicating that chromatin remodeling in the promoter region results in enhanced mAb gene transcription and q mAb . Similar beneficial effects of CI994 on mAb production were observed in mAb-expressing CS13-1.00 cells. Collectively, our findings indicate that CI994 increases mAb production in rCHO cell cultures by chromatin remodeling resulting from acetylation of histones in the mAb gene promoter. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Dongil Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Chansik Yoon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Gyun Min Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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Lin PC, Liu R, Alvin K, Wahyu S, Murgolo N, Ye J, Du Z, Song Z. Improving Antibody Production in Stably Transfected CHO Cells by CRISPR-Cas9-Mediated Inactivation of Genes Identified in a Large-Scale Screen with Chinese Hamster-Specific siRNAs. Biotechnol J 2020; 16:e2000267. [PMID: 33079482 DOI: 10.1002/biot.202000267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/25/2020] [Indexed: 11/07/2022]
Abstract
The Chinese hamster ovary (CHO) cell line is commonly used for the production of biotherapeutics. As cell productivity directly affects the cost of production, methods are developed to manipulate the expression of specific genes that are known to be involved in protein synthesis, folding, and secretion to increase productivity. However, there are no large-scale CHO-specific functional screens to identify novel gene targets that impact the production of secreted recombinant proteins. Here, a large-scale, CHO cell-specific small interfering RNA screen is performed to identify genes that consistently enhance antibody production when silenced in a panel of seven CHO cell lines. Four genes, namely, Cyp1a2, Atp5s, Dgki, and P3h2, are identified, and then selected for CRISPR-Cas9 knockout validation in recombinant CHO cell lines. Single knockout of Cyp1a2, Atp5s, or Dgki, but not P3h2, results in a more than 90% increase in specific antibody productivity. Overall, the knockout of Cyp1a2 demonstrates the most significant improvement of antibody production, with a minimal impact on cell growth.
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Affiliation(s)
- Pao-Chun Lin
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #04-01 Centros, Singapore, 138668, Singapore
| | - Ren Liu
- Cell Line Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Krista Alvin
- Cell Line Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Shahreel Wahyu
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #04-01 Centros, Singapore, 138668, Singapore
| | - Nicholas Murgolo
- Bioinformatics, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Jianxin Ye
- Cell Line Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Zhimei Du
- Cell Line Development, MRL, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Zhiwei Song
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #04-01 Centros, Singapore, 138668, Singapore
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