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Liu X, Chen Q, Yin X, Wang X, Ran J, Yu W, Wang B. Study on chromatin regulation patterns of expression vectors in the PhiC31 integration site. Epigenetics 2024; 19:2337085. [PMID: 38595049 PMCID: PMC11008548 DOI: 10.1080/15592294.2024.2337085] [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: 10/15/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
The PhiC31 integration system allows for targeted and efficient transgene integration and expression by recognizing pseudo attP sites in mammalian cells and integrating the exogenous genes into the open chromatin regions of active chromatin. In order to investigate the regulatory patterns of efficient gene expression in the open chromatin region of PhiC31 integration, this study utilized Ubiquitous Chromatin Opening Element (UCOE) and activating RNA (saRNA) to modulate the chromatin structure in the promoter region of the PhiC31 integration vector. The study analysed the effects of DNA methylation and nucleosome occupancy changes in the integrated promoter on gene expression levels. The results showed that for the OCT4 promoter with moderate CG density, DNA methylation had a smaller impact on expression compared to changes in nucleosome positioning near the transcription start site, which was crucial for enhancing downstream gene expression. On the other hand, for the SOX2 promoter with high CG density, increased methylation in the CpG island upstream of the transcription start site played a key role in affecting high expression, but the positioning and clustering of nucleosomes also had an important influence. In conclusion, analysing the DNA methylation patterns, nucleosome positioning, and quantity distribution of different promoters can determine whether the PhiC31 integration site possesses the potential to further enhance expression or overcome transgene silencing effects by utilizing chromatin regulatory elements.
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Affiliation(s)
- Xueli Liu
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
- Pharmaceutical Department, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Qina Chen
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Xudong Yin
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Xiao Wang
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Jinshan Ran
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
| | - Wei Yu
- Department of Pharmacy, 920th Hospital of Joint Logistics Support Force, PLA, Kunming, China
| | - Bin Wang
- Key Technology Engineering Center for New Veterinary Vaccine and Industry of Yunnan Provincial Education Department, Kunming University, Kunming, Yunnan, China
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Lee Z, Wan J, Shen A, Barnard G. Gene copy number, gene configuration and LC/HC mRNA ratio impact on antibody productivity and product quality in targeted integration CHO cell lines. Biotechnol Prog 2024; 40:e3433. [PMID: 38321634 DOI: 10.1002/btpr.3433] [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: 10/13/2023] [Revised: 12/01/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
The augmentation of transgene copy numbers is a prevalent approach presumed to enhance transcriptional activity and product yield. CHO cell lines engineered via targeted integration (TI) offer an advantageous platform for investigating the interplay between gene copy number, mRNA abundance, product yield, and product quality. Our investigation revealed that incrementally elevating the gene copy numbers of both IgG heavy chain (HC) and light chain (LC) concurrently resulted in the attainment of plateaus in mRNA levels and product titers, notably occurring beyond four to five gene copies integrated at the same TI site. Furthermore, maintaining a fixed gene copy number while varying the position of genes within the vector influenced the LC/HC mRNA ratio, which subsequently exerted a substantial impact on product titer. Moreover, manipulation of the LC/HC gene ratio through the introduction of surplus LC gene copies led to heightened LC mRNA expression and a reduction in the levels of high molecular weight species. It is noteworthy that the effects of excess LC on product titer were dependent on the specific molecule under consideration. The strategic utilization of PCR tags enabled precise quantification of transcription from each expression slot within the vector, facilitating the identification of highly expressive and less expressive slots. Collectively, these findings significantly enhance our understanding of stable antibody production in TI CHO cell lines.
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Affiliation(s)
- Zion Lee
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Jun Wan
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Amy Shen
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
| | - Gavin Barnard
- Department of Cell Culture and Bioprocess Operations, Genentech, Inc., San Francisco, California, USA
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Ghanim HY, Porteus MH. Gene regulation in inborn errors of immunity: Implications for gene therapy design and efficacy. Immunol Rev 2024; 322:157-177. [PMID: 38233996 DOI: 10.1111/imr.13305] [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: 09/22/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Inborn errors of immunity (IEI) present a unique paradigm in the realm of gene therapy, emphasizing the need for precision in therapeutic design. As gene therapy transitions from broad-spectrum gene addition to careful modification of specific genes, the enduring safety and effectiveness of these therapies in clinical settings have become crucial. This review discusses the significance of IEIs as foundational models for pioneering and refining precision medicine. We explore the capabilities of gene addition and gene correction platforms in modifying the DNA sequence of primary cells tailored for IEIs. The review uses four specific IEIs to highlight key issues in gene therapy strategies: X-linked agammaglobulinemia (XLA), X-linked chronic granulomatous disease (X-CGD), X-linked hyper IgM syndrome (XHIGM), and immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX). We detail the regulatory intricacies and therapeutic innovations for each disorder, incorporating insights from relevant clinical trials. For most IEIs, regulated expression is a vital aspect of the underlying biology, and we discuss the importance of endogenous regulation in developing gene therapy strategies.
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Affiliation(s)
- Hana Y Ghanim
- Division of Pediatrics, Division of Oncology, Hematology, Stem Cell Transplantation, Stanford University, Stanford, California, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew H Porteus
- Division of Pediatrics, Division of Oncology, Hematology, Stem Cell Transplantation, Stanford University, Stanford, California, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, California, USA
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Xu Y, Crowe KB, Lieske PL, Barnes M, Bandara K, Chu J, Wei W, Scarcelli JJ, Zhang L. A high-fidelity, dual site-specific integration system in CHO cells by a Bxb1 recombinase. Biotechnol J 2024; 19:e2300410. [PMID: 38375559 DOI: 10.1002/biot.202300410] [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: 08/14/2023] [Revised: 11/16/2023] [Accepted: 12/06/2023] [Indexed: 02/21/2024]
Abstract
Site-specific integration (SSI) via recombinase mediated cassette exchange (RMCE) has shown advantages over random integration methods for expression of biotherapeutics. As an extension of our previous work developing SSI host cells, we developed a dual-site SSI system having two independent integration sites at different genomic loci, each containing a unique landing pad (LP). This system was leveraged to generate and compare two RMCE hosts, one (dFRT) compatible with the Flp recombinase, the other (dBxb1) compatible with the Bxb1 recombinase. Our comparison demonstrated that the dBxb1 host was able to generate stable transfectant pools in a shorter time frame, and cells within the dBxb1 transfectant pools were more phenotypically and genotypically stable. We further improved process performance of the dBxb1 host, resulting in desired fed batch performance attributes. Clones derived from this improved host (referred as 41L-11) maintained stable expression profiles over extended generations. While the data represents a significant improvement in the efficiency of our cell line development process, the dual LP architecture also affords a high degree of flexibility for development of complex protein modalities.
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Affiliation(s)
- Yifeng Xu
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Kerstin B Crowe
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Paulena L Lieske
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Michael Barnes
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Kalpanie Bandara
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Jianlin Chu
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Wei Wei
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - John J Scarcelli
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
| | - Lin Zhang
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Science, Pfizer Inc, Andover, Massachusetts, USA
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