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Sukwattananipaat P, Kuroda H, Yamano-Adachi N, Omasa T. Metabolomic characterization of monoclonal antibody-producing Chinese hamster lung (CHL)-YN cells in glucose-controlled serum-free fed-batch operation. Biotechnol Bioeng 2024; 121:2848-2867. [PMID: 39138873 DOI: 10.1002/bit.28777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 08/15/2024]
Abstract
The fast-growing Chinese hamster lung (CHL)-YN cell line was recently developed for monoclonal antibody production. In this study, we applied a serum-free fed-batch cultivation process to immunoglobulin (Ig)G1-producing CHL-YN cells, which were then used to design a dynamic glucose supply system to stabilize the extracellular glucose concentration based on glucose consumption. Glucose consumption of the cultures rapidly oscillated following three phases of glutamine metabolism: consumption, production, and re-consumption. Use of the dynamic glucose supply prolonged the viability of the CHL-YN-IgG1 cell cultures and increased IgG1 production. Liquid chromatography with tandem mass spectrometry-based target metabolomics analysis of the extracellular metabolites during the first glutamine shift was conducted to search for depleted compounds. The results suggest that the levels of four amino acids, namely arginine, aspartate, methionine, and serine, were sharply decreased in CHL-YN cells during glutamine production. Supporting evidence from metabolic and gene expression analyses also suggest that CHL-YN cells acquired ornithine- and cystathionine-production abilities that differed from those in Chinese hamster ovary-K1 cells, potentially leading to proline and cysteine biosynthesis.
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Affiliation(s)
| | - Hirotaka Kuroda
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Shimadzu Corp., Kyoto, Japan
- Shimadzu Analytical Innovation Research Laboratories, Osaka, Japan
| | - Noriko Yamano-Adachi
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Manufacturing Technology Association of Biologics (MAB), Hyogo, Japan
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Manufacturing Technology Association of Biologics (MAB), Hyogo, Japan
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Elste J, Saini A, Mejia-Alvarez R, Mejía A, Millán-Pacheco C, Swanson-Mungerson M, Tiwari V. Significance of Artificial Intelligence in the Study of Virus-Host Cell Interactions. Biomolecules 2024; 14:911. [PMID: 39199298 PMCID: PMC11352483 DOI: 10.3390/biom14080911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 09/01/2024] Open
Abstract
A highly critical event in a virus's life cycle is successfully entering a given host. This process begins when a viral glycoprotein interacts with a target cell receptor, which provides the molecular basis for target virus-host cell interactions for novel drug discovery. Over the years, extensive research has been carried out in the field of virus-host cell interaction, generating a massive number of genetic and molecular data sources. These datasets are an asset for predicting virus-host interactions at the molecular level using machine learning (ML), a subset of artificial intelligence (AI). In this direction, ML tools are now being applied to recognize patterns in these massive datasets to predict critical interactions between virus and host cells at the protein-protein and protein-sugar levels, as well as to perform transcriptional and translational analysis. On the other end, deep learning (DL) algorithms-a subfield of ML-can extract high-level features from very large datasets to recognize the hidden patterns within genomic sequences and images to develop models for rapid drug discovery predictions that address pathogenic viruses displaying heightened affinity for receptor docking and enhanced cell entry. ML and DL are pivotal forces, driving innovation with their ability to perform analysis of enormous datasets in a highly efficient, cost-effective, accurate, and high-throughput manner. This review focuses on the complexity of virus-host cell interactions at the molecular level in light of the current advances of ML and AI in viral pathogenesis to improve new treatments and prevention strategies.
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Affiliation(s)
- James Elste
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
| | - Akash Saini
- Hinsdale Central High School, 5500 S Grant St, Hinsdale, IL 60521, USA;
| | - Rafael Mejia-Alvarez
- Department of Physiology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA;
| | - Armando Mejía
- Departamento de Biotechnology, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de Mexico 09340, Mexico;
| | - Cesar Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Av. Universidad No. 1001, Col Chamilpa, Cuernavaca 62209, Mexico;
| | - Michelle Swanson-Mungerson
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
| | - Vaibhav Tiwari
- Department of Microbiology & Immunology, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA; (J.E.); (M.S.-M.)
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Masuda K, Kubota M, Nakazawa Y, Iwama C, Watanabe K, Ishikawa N, Tanabe Y, Kono S, Tanemura H, Takahashi S, Makino T, Okumura T, Horiuchi T, Nonaka K, Murakami S, Kamihira M, Omasa T. Establishment of a novel cell line, CHO-MK, derived from Chinese hamster ovary tissues for biologics manufacturing. J Biosci Bioeng 2024; 137:471-479. [PMID: 38472071 DOI: 10.1016/j.jbiosc.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/04/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024]
Abstract
Chinese hamster ovary (CHO) cells are widely used as a host for producing recombinant therapeutic proteins due to advantages such as human-like post-translational modification, correct protein folding, higher productivity, and a proven track record in biopharmaceutical development. Much effort has been made to improve the process of recombinant protein production, in terms of its yield and productivity, using conventional CHO cell lines. However, to the best of our knowledge, no attempts have been made to acquire new CHO cell lines from Chinese hamster ovary. In this study, we established and characterized a novel CHO cell line, named CHO-MK, derived from freshly isolated Chinese hamster ovary tissues. Some immortalized cell lines were established via sub-culture derived from primary culture, one of which was selected for further development toward a unique expression system design. After adapting serum-free and suspension culture conditions, the resulting cell line exhibited a considerably shorter doubling time (approximately 10 h) than conventional CHO cell lines (approximately 20 h). Model monoclonal antibody (IgG1)-producing cells were generated, and the IgG1 concentration of fed-batch culture reached approximately 5 g/L on day 8 in a 200-L bioreactor. The cell bank of CHO-MK cells was prepared as a new host and assessed for contamination by adventitious agents, with the results indicating that it was free from any such contaminants, including infectious viruses. Taking these findings together, this study showed the potential of CHO-MK cells with a shorter doubling time/process time and enhanced productivity in biologics manufacturing.
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Affiliation(s)
- Kenji Masuda
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan; Manufacturing Technology Association of Biologics, 2-6-16 Shinkawa, Chuo-ku, Tokyo 104-0033, Japan
| | - Michi Kubota
- Manufacturing Technology Association of Biologics, 2-6-16 Shinkawa, Chuo-ku, Tokyo 104-0033, Japan; Chitose Laboratory Corp., KSP EAST511, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Yuto Nakazawa
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan
| | - Chigusa Iwama
- Manufacturing Technology Association of Biologics, 2-6-16 Shinkawa, Chuo-ku, Tokyo 104-0033, Japan; Chitose Laboratory Corp., KSP EAST511, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Kazuhiko Watanabe
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan
| | - Naoto Ishikawa
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan
| | - Yumiko Tanabe
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan
| | - Satoru Kono
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan
| | - Hiroki Tanemura
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan
| | - Shinichi Takahashi
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan
| | - Tomohiro Makino
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan
| | - Takeshi Okumura
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan; Manufacturing Technology Association of Biologics, 2-6-16 Shinkawa, Chuo-ku, Tokyo 104-0033, Japan
| | - Takayuki Horiuchi
- Chitose Laboratory Corp., KSP EAST511, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Koichi Nonaka
- Biologics Division, Biologics Technology Research Laboratories I, Daiichi Sankyo Co., Ltd., 2716-1 Kurakake, Akaiwa, Chiyoda-machi, Gunma 370-0503, Japan; Manufacturing Technology Association of Biologics, 2-6-16 Shinkawa, Chuo-ku, Tokyo 104-0033, Japan
| | - Sei Murakami
- Manufacturing Technology Association of Biologics, 2-6-16 Shinkawa, Chuo-ku, Tokyo 104-0033, Japan
| | - Masamichi Kamihira
- Manufacturing Technology Association of Biologics, 2-6-16 Shinkawa, Chuo-ku, Tokyo 104-0033, Japan; Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takeshi Omasa
- Manufacturing Technology Association of Biologics, 2-6-16 Shinkawa, Chuo-ku, Tokyo 104-0033, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Yamano-Adachi N, Hata H, Nakanishi Y, Omasa T. Effects of genome instability of parental CHO cell clones on chromosome number distribution and recombinant protein production in parent-derived subclones. J Biosci Bioeng 2024; 137:54-63. [PMID: 37981489 DOI: 10.1016/j.jbiosc.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023]
Abstract
Chinese hamster ovary (CHO) cells are the de facto standard host cells for biopharmaceuticals, and there is great interest in developing methods for constructing stable production cell lines. In this study, clones with a wide chromosome number distribution were selected from isolated antibody-producing strains, and subclones obtained from these clones were evaluated. The transgene copy number varied between the subclones. Even among subclones with similar copy numbers of antibody genes and maintained insertion sites, clones with different productivity were generated. Although the chromosome number distribution differed between these subclones, there was no correlation between the variability in chromosome number after cloning (genome instability) and productivity. Most of the subclones obtained from a parental strain with a wide chromosome number had the same wide chromosome number distribution as the parental strain. Less frequently, cells with less variation (remaining in one distribution) in chromosome number were isolated from cells with a wide chromosome number distribution, from which subclones with less variation in chromosome number were obtained when subcloning was performed again. These results imply that the characteristics of clones with chromosomal instability are inherited by subclones, and thus provide a better understanding of cell line stability/instability.
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Affiliation(s)
- Noriko Yamano-Adachi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hirofumi Hata
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuto Nakanishi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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5
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Amiri S, Adibzadeh S, Ghanbari S, Rahmani B, Kheirandish MH, Farokhi-Fard A, Dastjerdeh MS, Davami F. CRISPR-interceded CHO cell line development approaches. Biotechnol Bioeng 2023; 120:865-902. [PMID: 36597180 DOI: 10.1002/bit.28329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
For industrial production of recombinant protein biopharmaceuticals, Chinese hamster ovary (CHO) cells represent the most widely adopted host cell system, owing to their capacity to produce high-quality biologics with human-like posttranslational modifications. As opposed to random integration, targeted genome editing in genomic safe harbor sites has offered CHO cell line engineering a new perspective, ensuring production consistency in long-term culture and high biotherapeutic expression levels. Corresponding the remarkable advancements in knowledge of CRISPR-Cas systems, the use of CRISPR-Cas technology along with the donor design strategies has been pushed into increasing novel scenarios in cell line engineering, allowing scientists to modify mammalian genomes such as CHO cell line quickly, readily, and efficiently. Depending on the strategies and production requirements, the gene of interest can also be incorporated at single or multiple loci. This review will give a gist of all the most fundamental recent advancements in CHO cell line development, such as different cell line engineering approaches along with donor design strategies for targeted integration of the desired construct into genomic hot spots, which could ultimately lead to the fast-track product development process with consistent, improved product yield and quality.
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Affiliation(s)
- Shahin Amiri
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Setare Adibzadeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Samaneh Ghanbari
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnaz Rahmani
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad H Kheirandish
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies, Tehran University of Medical Sciences, Tehran, Iran
| | - Aref Farokhi-Fard
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansoureh S Dastjerdeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Davami
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Kawabe Y, Kamihira M. Novel cell lines derived from Chinese hamster kidney tissue. PLoS One 2022; 17:e0266061. [PMID: 35358245 PMCID: PMC8970510 DOI: 10.1371/journal.pone.0266061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/13/2022] [Indexed: 01/15/2023] Open
Abstract
Immortalized kidney cell lines are widely used in basic and applied research such as cell permeability tests and drug screening. Although many cell lines have been established from kidney tissues, the immortalization process has not been clarified in these cell lines. In this study, we analyzed the phenotypic changes that occurred during the immortalization of kidney cells derived from Chinese hamster tissue in terms of karyotype and gene expression profiles. In the newly established cell line, designated as CHK-Q, gene expression profiles at each stage of the immortalization process and during the adaptation to serum-free conditions were analyzed by DNA microarray. Renal stem cell markers CD24 and CD133 were expressed in CHK-Q cells, suggesting that CHK-Q cells were transformed from renal stem cells. Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis to identify the pathways of upregulated and downregulated genes revealed that the immortalization of CHK-Q cells was associated with increased fluctuations in the expression of specific proto-oncogenes. Karyotype analysis of spontaneously immortalized CHK-Q cells indicated that CHK-Q chromosomes had a typical modal number of 23 but possessed slight chromosomal abnormalities. In this study, we investigated the mechanism of cell environmental adaptation by analyzing gene expression behavior during the immortalization process and serum-free adaptation. CHK-Q cells are applicable to the fields of biotechnology and biomedical science by utilizing their characteristics as kidney-derived cells.
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Affiliation(s)
- Yoshinori Kawabe
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan
- Manufacturing Technology Association of Biologics, Kobe, Japan
| | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, Fukuoka, Japan
- Manufacturing Technology Association of Biologics, Kobe, Japan
- * E-mail:
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