1
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Wang Y, Fu Q, Park SY, Lee YS, Park SY, Lee DY, Yoon S. Decoding cellular mechanism of recombinant adeno-associated virus (rAAV) and engineering host-cell factories toward intensified viral vector manufacturing. Biotechnol Adv 2024; 71:108322. [PMID: 38336188 DOI: 10.1016/j.biotechadv.2024.108322] [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: 06/11/2023] [Revised: 01/22/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Recombinant adeno-associated virus (rAAV) is one of the prominent gene delivery vehicles that has opened promising opportunities for novel gene therapeutic approaches. However, the current major viral vector production platform, triple transfection in mammalian cells, may not meet the increasing demand. Thus, it is highly required to understand production bottlenecks from the host cell perspective and engineer the cells to be more favorable and tolerant to viral vector production, thereby effectively enhancing rAAV manufacturing. In this review, we provided a comprehensive exploration of the intricate cellular process involved in rAAV production, encompassing various stages such as plasmid entry to the cytoplasm, plasmid trafficking and nuclear delivery, rAAV structural/non-structural protein expression, viral capsid assembly, genome replication, genome packaging, and rAAV release/secretion. The knowledge in the fundamental biology of host cells supporting viral replication as manufacturing factories or exhibiting defending behaviors against viral production is summarized for each stage. The control strategies from the perspectives of host cell and materials (e.g., AAV plasmids) are proposed as our insights based on the characterization of molecular features and our existing knowledge of the AAV viral life cycle, rAAV and other viral vector production in the Human embryonic kidney (HEK) cells.
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Affiliation(s)
- Yongdan Wang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Qiang Fu
- Department of Biomedical Engineering and Biotechnology, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - So Young Park
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, University of Massachusetts Lowell, Lowell, MA 01854, United States of America
| | - Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States of America.
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2
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Inwood S, Cheng K, Betenbaugh MJ, Shiloach J. Genome-Wide High-Throughput RNAi Screening for Identification of Genes Involved in Protein Production. Methods Mol Biol 2024; 2810:317-327. [PMID: 38926288 DOI: 10.1007/978-1-0716-3878-1_20] [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] [Indexed: 06/28/2024]
Abstract
With an increasing number of blockbuster drugs being recombinant mammalian proteins, protein production platforms that focus on mammalian proteins have had a profound impact in many areas of basic and applied research. Many groups, both academic and industrial, have been focusing on developing cost-effective methods to improve the production of mammalian proteins that would support potential therapeutic applications. As it stands, while a wide range of platforms have been successfully developed for laboratory use, the majority of biologicals are still produced in mammalian cell lines due to the requirement for posttranslational modification and the biosynthetic complexity of target proteins. An unbiased high-throughput RNAi screening approach can be an efficient tool to identify target genes involved in recombinant protein production. Here, we describe the process of optimizing the transfection conditions, performing the genome-wide siRNA screen, the activity and cell viability assays, and the validation transfection to identify genes involved with protein expression.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, MD, USA
| | - Ken Cheng
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Rockville, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, MD, USA.
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3
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Abaandou L, Quan D, Shiloach J. Affecting HEK293 Cell Growth and Production Performance by Modifying the Expression of Specific Genes. Cells 2021; 10:cells10071667. [PMID: 34359846 PMCID: PMC8304725 DOI: 10.3390/cells10071667] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022] Open
Abstract
The HEK293 cell line has earned its place as a producer of biotherapeutics. In addition to its ease of growth in serum-free suspension culture and its amenability to transfection, this cell line’s most important attribute is its human origin, which makes it suitable to produce biologics intended for human use. At the present time, the growth and production properties of the HEK293 cell line are inferior to those of non-human cell lines, such as the Chinese hamster ovary (CHO) and the murine myeloma NSO cell lines. However, the modification of genes involved in cellular processes, such as cell proliferation, apoptosis, metabolism, glycosylation, secretion, and protein folding, in addition to bioprocess, media, and vector optimization, have greatly improved the performance of this cell line. This review provides a comprehensive summary of important achievements in HEK293 cell line engineering and on the global engineering approaches and functional genomic tools that have been employed to identify relevant genes for targeted engineering.
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Affiliation(s)
- Laura Abaandou
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
- Department of Chemistry and Biochemistry, College of Science, George Mason University, Fairfax, VA 22030, USA
| | - David Quan
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
| | - Joseph Shiloach
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
- Correspondence:
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4
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Samoudi M, Masson HO, Kuo CC, Robinson CM, Lewis NE. From omics to Cellular mechanisms in mammalian cell factory development. Curr Opin Chem Eng 2021; 32:100688. [PMID: 37475722 PMCID: PMC10357924 DOI: 10.1016/j.coche.2021.100688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mammalian cells have been used widely as biopharmaceutical cell factories due to their ability to make complex biotherapeutic proteins with human-compatible modifications. However, their application for some products has been hampered by low protein yields. Numerous studies have aimed to characterize cellular bottlenecks in the hope of boosting protein productivity, but the complexity of the underlying pathways and the diversity of the modifications have complicated cell engineering when relying solely on traditional methodologies. Incorporating omics-based and systems approaches into cell engineering can provide valuable insights into desirable phenotypes of cell factories. Here, we discuss cell engineering strategies for enhancing protein productivity in mammalian cell factories, particularly CHO and HEK293, and the opportunities and limitations of the genome-wide screening and multi-omics approaches for guiding cell engineering. Systems biology strategies will also be discussed to show how they refine our understanding of the cellular mechanisms which will aid in effective engineering strategies.
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Affiliation(s)
- Mojtaba Samoudi
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Helen O. Masson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Chih-Chung Kuo
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Caressa M Robinson
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- National Biologics Facility, Technical University of Denmark, Kgs. Lyngby, Denmark
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5
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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] [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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6
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Abaandou L, Sharma AK, Shiloach J. Knockout of the caspase 8-associated protein 2 gene improves recombinant protein expression in HEK293 cells through up-regulation of the cyclin-dependent kinase inhibitor 2A gene. Biotechnol Bioeng 2020; 118:186-198. [PMID: 32910455 DOI: 10.1002/bit.27561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/29/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Cell lines used in bioproduction are routinely engineered to improve their production efficiency. Numerous strategies, such as random mutagenesis, RNA interference screens, and transcriptome analyses have been employed to identify effective engineering targets. A genome-wide small interfering RNA screen previously identified the CASP8AP2 gene as a potential engineering target for improved expression of recombinant protein in the HEK293 cell line. Here, we validate the CASP8AP2 gene as an engineering target in HEK293 cells by knocking it out using CRISPR/Cas9 genome editing and assessing the effect of its knockout on recombinant protein expression, cell growth, cell viability, and overall gene expression. HEK293 cells lacking CASP8AP2 showed a seven-fold increase in specific expression of recombinant luciferase and a 2.5-fold increase in specific expression of recombinant SEAP, without significantly affecting cell growth and viability. Transcriptome analysis revealed that the deregulation of the cell cycle, specifically the upregulation of the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene, contributed to the improvement in recombinant protein expression in CASP8AP2 deficient cells. The results validate the CASP8AP2 gene is a viable engineering target for improved recombinant protein expression in the HEK293 cell line.
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Affiliation(s)
- Laura Abaandou
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland, USA.,Department of Chemistry and Biochemistry, George Mason University, Fairfax, VA, USA
| | - Ashish K Sharma
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland, USA
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7
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Mita P, Sun X, Fenyö D, Kahler DJ, Li D, Agmon N, Wudzinska A, Keegan S, Bader JS, Yun C, Boeke JD. BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. Nat Struct Mol Biol 2020; 27:179-191. [PMID: 32042152 PMCID: PMC7082080 DOI: 10.1038/s41594-020-0374-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) is the only autonomous retrotransposon active in human cells. Different host factors have been shown to influence L1 mobility however, systematic analyses of these factors are limited. Here, we developed a high-throughput microscopy-based retrotransposition assay that identified the Double-Stranded Break (DSB) repair and Fanconi Anemia factors active in the S/G2 phase as potent inhibitors and regulators of L1 activity. In particular BRCA1, an E3 ubiquitin ligase with a key role in several DNA repair pathways, directly affects L1 retrotransposition frequency and structure and also plays a distinct role in controlling L1 ORF2 protein translation through L1 mRNA binding. These results suggest the existence of a “battleground” at the DNA replication fork between HR factors and L1 retrotransposons, and revealing a potential role for L1 in the genotypic evolution of tumors characterized by BRCA1 and HR repair deficiencies.
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Affiliation(s)
- Paolo Mita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,Cellarity Inc., Cambridge, MA, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - David J Kahler
- High Throughput Biology Core, NYU Langone Health, New York, NY, USA.,Planet Pharma, Boston, MA, USA
| | - Donghui Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,Flagship VL58, Inc., Cambridge, MA, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Chi Yun
- High Throughput Biology Core, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
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8
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Inwood S, Abaandou L, Betenbaugh M, Shiloach J. Improved protein expression in HEK293 cells by over-expressing miR-22 and knocking-out its target gene, HIPK1. N Biotechnol 2019; 54:28-33. [PMID: 31425885 DOI: 10.1016/j.nbt.2019.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/01/2019] [Accepted: 08/15/2019] [Indexed: 02/08/2023]
Abstract
Stable cell lines can continuously produce a recombinant protein without the need to repeatedly engineer the genome. In a previous study HIPK1, Homeodomain-interacting Protein Kinase 1, was found to be a target of the microRNA miR-22 that, when repressed, improved expression of both an intracellular and a secreted protein. In this report, HEK293 cells stably over-expressing miR-22 were compared with HEK293 with knockout of HIPK1, executed by CRISPR/Cas9, for their ability to improve recombinant protein expression. In this model case of luciferase, over-expression of miR-22 improved overall activity 2.4-fold while the HIPK1 knockout improved overall activity 4.7-fold.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA; Department of Chemical and Biomolecular Engineering Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Laura Abaandou
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA.
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9
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Klanert G, Fernandez DJ, Weinguny M, Eisenhut P, Bühler E, Melcher M, Titus SA, Diendorfer AB, Gludovacz E, Jadhav V, Xiao S, Stern B, Lal M, Shiloach J, Borth N. A cross-species whole genome siRNA screen in suspension-cultured Chinese hamster ovary cells identifies novel engineering targets. Sci Rep 2019; 9:8689. [PMID: 31213643 PMCID: PMC6582146 DOI: 10.1038/s41598-019-45159-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 05/29/2019] [Indexed: 12/16/2022] Open
Abstract
High-throughput siRNA screens were only recently applied to cell factories to identify novel engineering targets which are able to boost cells towards desired phenotypes. While siRNA libraries exist for model organisms such as mice, no CHO-specific library is publicly available, hindering the application of this technique to CHO cells. The optimization of these cells is of special interest, as they are the main host for the production of therapeutic proteins. Here, we performed a cross-species approach by applying a mouse whole-genome siRNA library to CHO cells, optimized the protocol for suspension cultured cells, as this is the industrial practice for CHO cells, and developed an in silico method to identify functioning siRNAs, which also revealed the limitations of using cross-species libraries. With this method, we were able to identify several genes that, upon knockdown, enhanced the total productivity in the primary screen. A second screen validated two of these genes, Rad21 and Chd4, whose knockdown was tested in additional CHO cell lines, confirming the induced high productivity phenotype, but also demonstrating the cell line/clone specificity of engineering effects.
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Affiliation(s)
- Gerald Klanert
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Marcus Weinguny
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Eisenhut
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eugen Bühler
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA
| | - Michael Melcher
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Steven A Titus
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA
| | | | - Elisabeth Gludovacz
- University of Natural Resources and Life Sciences, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Vaibhav Jadhav
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Su Xiao
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, USA
| | - Beate Stern
- Department of Biomedicine, University of Bergen, Bergen, Norway
- UniTargetingResearch AS, Bergen, Norway
| | - Madhu Lal
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, USA.
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Graz, Austria.
- University of Natural Resources and Life Sciences, Vienna, Austria.
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10
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Abaandou L, Shiloach J. Knocking out Ornithine Decarboxylase Antizyme 1 ( OAZ1) Improves Recombinant Protein Expression in the HEK293 Cell Line. Med Sci (Basel) 2018; 6:medsci6020048. [PMID: 29890687 PMCID: PMC6024716 DOI: 10.3390/medsci6020048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
Creating efficient cell lines is a priority for the biopharmaceutical industry, which produces biologicals for various uses. A recent approach to achieving this goal is the use of non-coding RNAs, microRNA (miRNA) and small interfering RNA (siRNA), to identify key genes that can potentially improve production or growth. The ornithine decarboxylase antizyme 1 (OAZ1) gene, a negative regulator of polyamine biosynthesis, was identified in a genome-wide siRNA screen as a potential engineering target, because its knock down by siRNA increased recombinant protein expression from human embryonic kidney 293 (HEK293) cells by two-fold. To investigate this further, the OAZ1 gene in HEK293 cells was knocked out using CRISPR genome editing. The OAZ1 knockout cell lines displayed up to four-fold higher expression of both stably and transiently expressed proteins, with comparable growth and metabolic activity to the parental cell line; and an approximately three-fold increase in intracellular polyamine content. The results indicate that genetic inactivation of OAZ1 in HEK293 cells is an effective strategy to improve recombinant protein expression in HEK293 cells.
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Affiliation(s)
- Laura Abaandou
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, VA 22030, USA.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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11
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Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells. Genes (Basel) 2018; 9:genes9010025. [PMID: 29315258 PMCID: PMC5793178 DOI: 10.3390/genes9010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 12/27/2022] Open
Abstract
The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO) cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK), while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.
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12
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Inwood S, Betenbaugh MJ, Lal M, Shiloach J. Genome-Wide High-Throughput RNAi Screening for Identification of Genes Involved in Protein Production. Methods Mol Biol 2018; 1850:209-219. [PMID: 30242689 PMCID: PMC9563094 DOI: 10.1007/978-1-4939-8730-6_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
With an increasing number of blockbuster drugs being recombinant mammalian proteins, protein production platforms that focus on mammalian proteins have had a profound impact in many areas of basic and applied research. Many groups, both academic and industrial, have been focusing on developing cost-effective methods to improve the production of mammalian proteins that would support potential therapeutic applications. As it stands, while a wide range of platforms have been successfully developed for laboratory use, the majority of biologicals are still produced in mammalian cell lines due to the requirement for posttranslational modification and the biosynthetic complexity of target proteins. An unbiased high-throughput RNAi screening approach can be an efficient tool to identify target genes involved in recombinant protein production. Here we describe the process of optimizing the transfection conditions, performing the genome-wide siRNA screen, the activity and cell viability assays and the validation transfection to identify genes involved with protein expression.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Madhu Lal
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, MD, USA.
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13
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Genetic Architecture and Candidate Genes Identified for Follicle Number in Chicken. Sci Rep 2017; 7:16412. [PMID: 29180824 PMCID: PMC5703906 DOI: 10.1038/s41598-017-16557-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/14/2017] [Indexed: 11/08/2022] Open
Abstract
Follicular development has a major impact on reproductive performance. Most previous researchers focused on molecular mechanisms of follicular development. The genetic architecture underlying the number of follicle, however, has yet not to be thoroughly defined in chicken. Here we report a genome-wide association study for the genetic architecture determining the numbers of follicles in a large F2 resource population. The results showed heritability were low to moderate (0.05-0.28) for number of pre-ovulatory follicles (POF), small yellow follicles (SYF) and atresia follicles (AF). The highly significant SNPs associated with SYF were mainly located on GGA17 and GGA28. Only four significant SNPs were identified for POF on GGA1. The variance partitioned across chromosomes and chromosome lengths had a linear relationship for SYF (R2 = 0.58). The enriched genes created by the closest correspondent significant SNPs were found to be involved in biological pathways related to cell proliferation, cell cycle and cell survival. Two promising candidate genes, AMH and RGS3, were suggested to be prognostic biomarkers for SYF. In conclusion, this study offers the first evidence of genetic variance and positional candidate genes which influence the number of SYF in chicken. These identified informative SNPs may facilitate selection for an improved reproductive performance of laying hens.
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Inwood S, Buehler E, Betenbaugh M, Lal M, Shiloach J. Identifying HIPK1 as Target of miR-22-3p Enhancing Recombinant Protein Production From HEK 293 Cell by Using Microarray and HTP siRNA Screen. Biotechnol J 2017; 13. [PMID: 28987030 DOI: 10.1002/biot.201700342] [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: 05/08/2017] [Revised: 09/11/2017] [Indexed: 01/20/2023]
Abstract
Protein expression from human embryonic kidney cells (HEK 293) is an important tool for structural and clinical studies. It is previously shown that microRNAs (small, noncoding RNAs) are effective means for improved protein expression from these cells, and by conducting a high-throughput screening of the human microRNA library, several microRNAs are identified as potential candidates for improving expression. From these, miR-22-3p is chosen for further study since it increased the expression of luciferase, two membrane proteins and a secreted fusion protein with minimal effect on the cells' growth and viability. Since each microRNA can interact with several gene targets, it is of interest to identify the repressed genes for understanding and exploring the improved expression mechanism for further implementation. Here, the authors describe a novel approach for identification of the target genes by integrating the differential gene expression analysis with information obtained from our previously conducted high-throughput siRNA screening. The identified genes were validated as being involved in improving luciferase expression by using siRNA and qRT-PCR. Repressing the target gene, HIPK1, is found to increase luciferase and GPC3 expression 3.3- and 2.2-fold, respectively.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland 20892, USA.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Eugen Buehler
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Madhu Lal
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland 20892, USA
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Kang B, Jiang D, Ma R, He H, Yi Z, Chen Z. OAZ1 knockdown enhances viability and inhibits ER and LHR transcriptions of granulosa cells in geese. PLoS One 2017; 12:e0175016. [PMID: 28362829 PMCID: PMC5376318 DOI: 10.1371/journal.pone.0175016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/20/2017] [Indexed: 11/18/2022] Open
Abstract
An increasing number of studies suggest that ornithine decarboxylase antizyme 1 (OAZ1), which is regarded as a tumor suppressor gene, regulates follicular development, ovulation, and steroidogenesis. The granulosa cells in the ovary play a critical role in these ovarian functions. However, the action of OAZ1 mediating physiological functions of granulosa cells is obscure. OAZ1 knockdown in granulosa cells of geese was carried out in the current study. The effect of OAZ1 knockdown on polyamine metabolism, cell proliferation, apoptosis, and hormone receptor transcription of primary granulosa cells in geese was measured. The viability of granulosa cells transfected with the shRNA OAZ1 at 48 h was significantly higher than the control (p<0.05). The level of putrescine and spermidine in granulosa cells down-regulating OAZ1 was 7.04- and 2.11- fold higher compared with the control, respectively (p<0.05). The CCND1, SMAD1, and BCL-2 mRNA expression levels in granulosa cells down-regulating OAZ1 were each significantly higher than the control, respectively (p<0.05), whereas the PCNA and CASPASE 3 expression levels were significantly lower than the control (p<0.05). The estradiol concentration, ER and LHR mRNA expression levels were significantly lower in granulosa cells down-regulating OAZ1 compared with the control (p<0.05). Taken together, our results indicated that OAZ1 knockdown elevated the putrescine and spermidine contents and enhanced granulosa cell viability and inhibited ER and LHR transcriptions of granulosa cells in geese.
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Affiliation(s)
- Bo Kang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, People’s Republic of China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (BK); (DMJ)
| | - Dongmei Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, People’s Republic of China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan Province, People’s Republic of China
- * E-mail: (BK); (DMJ)
| | - Rong Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, People’s Republic of China
| | - Hui He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, People’s Republic of China
| | - Zhixin Yi
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, People’s Republic of China
| | - Ziyu Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, People’s Republic of China
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16
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Effect of Oaz1 overexpression on goose ovarian granulosa cells. Amino Acids 2017; 49:1123-1132. [DOI: 10.1007/s00726-017-2411-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/09/2017] [Indexed: 12/13/2022]
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