1
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Taghizadegan N, Firoozrai M, Nassiri M, Ariannejad H. A novel strategy for engineering of a smart generation of immune ribonucleases against EGFR + cells. J Cell Physiol 2021; 236:4303-4312. [PMID: 33421131 DOI: 10.1002/jcp.30118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/04/2020] [Accepted: 10/06/2020] [Indexed: 12/26/2022]
Abstract
The overexpression of epidermal growth factor receptor (EGFR) could result in the development of solid tumors of prostate, breast, gastric, colorectal, ovarian, and head and neck, leading to carcinoma. Antibody therapies are ideal methods to overcome malignant diseases. However, immunoribonucleases are a new generation of antibodies in which an RNase binds to a specific antibody and shows a stronger ability to terminate cancer cells. In this study, we engineered Rana pipiens RNase to bind to the scFv of human antiepidermal growth factor receptor antibody. The molecular dynamic simulations confirmed protein stability and the ability of scFv-ranpirnase (rantoxin) to bind to epidermal growth factor receptor protein. Then, the rantoxin construct was synthesized in a pCDNA 3.1 Neo vector. CHO-K1 cells were used as expression hosts and the construct was transfected. Cells were selected by antibiotic therapies using neomycin, 120 mg/ml, and the high-yield colony was screened by real-time polymerase chain reaction (PCR) methods. Then, the recombinant protein production was confirmed using the sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blot analyses. The molecular dynamic simulation (MDS) confirmed that the I467, S468, Q408, and H409 amino acids of EGFR bonded well to rantoxin. As revealed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and western blot analyses, the rantoxin production and PCR analysis showed that the T3 colony can produce rantoxin messenger RNA fourfold higher than the GAPDH gene. The immunotoxin function was assessed in A431 cancer cells and EGFR-negative HEK293 cells, and IC50 values were estimated to be 22.4 ± 3 and >620.4 ± 5 nM, respectively. The results indicated that the immunotoxins produced in this study had the potential for use as anticancer drugs.
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Affiliation(s)
- Nooshin Taghizadegan
- Department of Biochemistry, Shahrood Branch, Islamic Azad University, Shahrood, Iran
| | - Mohsen Firoozrai
- Department of Biochemistry, Shahrood Branch, Islamic Azad University, Shahrood, Iran
| | | | - Hamid Ariannejad
- Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
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2
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Nakayama Y, Adachi K, Shioda N, Maeta S, Nanba E, Kugoh H. Establishment of FXS-A9 panel with a single human X chromosome from fragile X syndrome-associated individual. Exp Cell Res 2020; 398:112419. [PMID: 33296661 DOI: 10.1016/j.yexcr.2020.112419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022]
Abstract
Fragile X syndrome (FXS) is the most common inheritable form of intellectual disability. FMR1, the gene responsible for FXS, is located on human chromosome Xq27.3 and contains a stretch of CGG trinucleotide repeats in its 5' untranslated region. FXS is caused by CGG repeats that expand beyond 200, resulting in FMR1 silencing via promoter hypermethylation. The molecular mechanism underlying CGG repeat expansion, a fundamental cause of FXS, remains poorly understood, partly due to a lack of experimental systems. Accumulated evidence indicates that the large chromosomal region flanking a CGG repeat is critical for repeat dynamics. In the present study, we isolated and introduced whole human X chromosomes from healthy, FXS premutation carriers, or FXS patients who carried disease condition-associated CGG repeat lengths, into mouse A9 cells via microcell-mediated chromosome transfer. The CGG repeat length-associated methylation status and human FMR1 expression in these monochromosomal hybrid cells mimicked those in humans. Thus, this set of A9 cells containing CGG repeats from three different origins (FXS-A9 panel) may provide a valuable resource for investigating a series of genetic and epigenetic CGG repeat dynamics during FXS pathogenesis.
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Affiliation(s)
- Yuji Nakayama
- Division of Radioisotope Science, Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Kaori Adachi
- Division of Genomic Science, Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Nofirifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Shoya Maeta
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Eiji Nanba
- Office for Research Strategy, Organization for Research Initiative and Promotion, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan
| | - Hiroyuki Kugoh
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan; Chromosome Engineering Research Center, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan.
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3
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An efficient protein production system via gene amplification on a human artificial chromosome and the chromosome transfer to CHO cells. Sci Rep 2019; 9:16954. [PMID: 31740706 PMCID: PMC6861226 DOI: 10.1038/s41598-019-53116-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/28/2019] [Indexed: 11/08/2022] Open
Abstract
Gene amplification methods play a crucial role in establishment of cells that produce high levels of recombinant protein. However, the stability of such cell lines and the level of recombinant protein produced continue to be suboptimal. Here, we used a combination of a human artificial chromosome (HAC) vector and initiation region (IR)/matrix attachment region (MAR) gene amplification method to establish stable cells that produce high levels of recombinant protein. Amplification of Enhanced green fluorescent protein (EGFP) was induced on a HAC carrying EGFP gene and IR/MAR sequences (EGFP MAR-HAC) in CHO DG44 cells. The expression level of EGFP increased approximately 6-fold compared to the original HAC without IR/MAR sequences. Additionally, anti-vascular endothelial growth factor (VEGF) antibody on a HAC (VEGF MAR-HAC) was also amplified by utilization of this IR/MAR-HAC system, and anti-VEGF antibody levels were approximately 2-fold higher compared with levels in control cells without IR/MAR. Furthermore, the expression of anti-VEGF antibody with VEGF MAR-HAC in CHO-K1 cells increased 2.3-fold compared with that of CHO DG44 cells. Taken together, the IR/MAR-HAC system facilitated amplification of a gene of interest on the HAC vector, and could be used to establish a novel cell line that stably produced protein from mammalian cells.
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Singh N, Herzer S. Downstream Processing Technologies/Capturing and Final Purification : Opportunities for Innovation, Change, and Improvement. A Review of Downstream Processing Developments in Protein Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 165:115-178. [PMID: 28795201 DOI: 10.1007/10_2017_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Increased pressure on upstream processes to maximize productivity has been crowned with great success, although at the cost of shifting the bottleneck to purification. As drivers were economical, focus is on now on debottlenecking downstream processes as the main drivers of high manufacturing cost. Devising a holistically efficient and economical process remains a key challenge. Traditional and emerging protein purification strategies with particular emphasis on methodologies implemented for the production of recombinant proteins of biopharmaceutical importance are reviewed. The breadth of innovation is addressed, as well as the challenges the industry faces today, with an eye to remaining impartial, fair, and balanced. In addition, the scope encompasses both chromatographic and non-chromatographic separations directed at the purification of proteins, with a strong emphasis on antibodies. Complete solutions such as integrated USP/DSP strategies (i.e., continuous processing) are discussed as well as gains in data quantity and quality arising from automation and high-throughput screening (HTS). Best practices and advantages through design of experiments (DOE) to access a complex design space such as multi-modal chromatography are reviewed with an outlook on potential future trends. A discussion of single-use technology, its impact and opportunities for further growth, and the exciting developments in modeling and simulation of DSP rounds out the overview. Lastly, emerging trends such as 3D printing and nanotechnology are covered. Graphical Abstract Workflow of high-throughput screening, design of experiments, and high-throughput analytics to understand design space and design space boundaries quickly. (Reproduced with permission from Gregory Barker, Process Development, Bristol-Myers Squibb).
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Affiliation(s)
- Nripen Singh
- Bristol-Myers Squibb, Global Manufacturing and Supply, Devens, MA, 01434, USA.
| | - Sibylle Herzer
- Bristol-Myers Squibb, Global Manufacturing and Supply, Hopewell, NJ, 01434, USA
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5
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Zamanian S, Mohammadi-Yeganeh S, Kia V, Kaghazian H, Paryan M. Design and validation of a new method to detect and quantify residual host cell DNA in human recombinant erythropoietin (rEPO). Prep Biochem Biotechnol 2017; 47:847-851. [PMID: 28426392 DOI: 10.1080/10826068.2017.1320292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
During the purification of human recombinant erythropoietin (rEPO) from host cells, residual DNA may remain in final products. This contamination is a risk factor for patients and may result in the inactivation of some tumor suppressor genes or activation of oncogenes if its concentration is more than the standard defined by WHO. Based on WHO's criteria, acceptable level of residual DNA in biopharmaceuticals is less than 10-100 pg/dose. In this study, we have designed a sensitive and specific quantitative real-time polymerase chain reaction (PCR) assay for the detection of residual DNA in human rEPO products. All reported sequences of CHO's GAPDH gene were retrieved from GenBank, and a multiple alignment was performed using Mega 6 software to find conserved regions of the gene. Primers and probe were designed by AlleleID7 software for the highly conserved region. Quantitative real-time PCR showed an R2 value more than 0.99 and the efficiency equal to 101% indicating a highly accurate and efficiency of the reaction, respectively. Based on the standard curve, the limit of detection of the assay was determined to be 10 copies/µL (0.00967 fg/µL). In addition, the inter- and intra-assay of the test were determined to be 1.14% and 0.65%, respectively, which are in acceptable range according to the WHO's guidelines.
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Affiliation(s)
- Shima Zamanian
- a Faculty of Science, University of Guilan , Department of Biology , Rasht , Iran
| | - Samira Mohammadi-Yeganeh
- b Cellular and Molecular Biology Research Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran.,c Department of Biotechnology, School of Advanced Technologies in Medicine , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Vahid Kia
- d Faculty of Medicine, Department of Medical Biotechnology , Zanjan University of Medical Sciences , Zanjan , Iran
| | - Hooman Kaghazian
- e Department of Research and Development, Production and Research Complex , Pasteur Institute of Iran , Tehran , Iran
| | - Mahdi Paryan
- e Department of Research and Development, Production and Research Complex , Pasteur Institute of Iran , Tehran , Iran
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6
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Ferro S, Fabre I, Chenivesse X. Optimizing a Method for the Quantification by Quantitative Real-Time Polymerase Chain Reaction of Host Cell DNA in Plasmid Vector Batches Used in Human Gene Therapy. Hum Gene Ther Methods 2016; 27:159-70. [DOI: 10.1089/hgtb.2015.155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Serge Ferro
- Laboratory Controls Division, French National Agency for Medicines and Health Products Safety, Vendargues, France
| | - Isabelle Fabre
- Laboratory Controls Division, French National Agency for Medicines and Health Products Safety, Vendargues, France
| | - Xavier Chenivesse
- Laboratory Controls Division, French National Agency for Medicines and Health Products Safety, Vendargues, France
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7
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André M, Reghin S, Boussard E, Lempereur L, Maisonneuve S. Universal real-time PCR assay for quantitation and size evaluation of residual cell DNA in human viral vaccines. Biologicals 2016; 44:139-49. [DOI: 10.1016/j.biologicals.2016.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/26/2015] [Accepted: 03/05/2016] [Indexed: 12/15/2022] Open
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8
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Rosa SA, dos Santos R, Aires-Barros MR, Azevedo AM. Phenylboronic acid chromatography provides a rapid, reproducible and easy scalable multimodal process for the capture of monoclonal antibodies. Sep Purif Technol 2016. [DOI: 10.1016/j.seppur.2016.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Kinna A, Tolner B, Rota EM, Titchener-Hooker N, Nesbeth D, Chester K. IMAC capture of recombinant protein from unclarified mammalian cell feed streams. Biotechnol Bioeng 2016; 113:130-40. [PMID: 26174988 PMCID: PMC4737217 DOI: 10.1002/bit.25705] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/30/2015] [Accepted: 07/10/2015] [Indexed: 12/25/2022]
Abstract
Fusion-tag affinity chromatography is a key technique in recombinant protein purification. Current methods for protein recovery from mammalian cells are hampered by the need for feed stream clarification. We have developed a method for direct capture using immobilized metal affinity chromatography (IMAC) of hexahistidine (His6) tagged proteins from unclarified mammalian cell feed streams. The process employs radial flow chromatography with 300-500 μm diameter agarose resin beads that allow free passage of cells but capture His-tagged proteins from the feed stream; circumventing expensive and cumbersome centrifugation and/or filtration steps. The method is exemplified by Chinese Hamster Ovary (CHO) cell expression and subsequent recovery of recombinant His-tagged carcinoembryonic antigen (CEA); a heavily glycosylated and clinically relevant protein. Despite operating at a high NaCl concentration necessary for IMAC binding, cells remained over 96% viable after passage through the column with host cell proteases and DNA detected at ∼ 8 U/mL and 2 ng/μL in column flow-through, respectively. Recovery of His-tagged CEA from unclarified feed yielded 71% product recovery. This work provides a basis for direct primary capture of fully glycosylated recombinant proteins from unclarified mammalian cell feed streams.
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Affiliation(s)
- Alexander Kinna
- Department of Oncology, University College London, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK
- Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Berend Tolner
- Department of Oncology, University College London, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK
| | - Enrique Miranda Rota
- Department of Oncology, University College London, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK
| | - Nigel Titchener-Hooker
- Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Darren Nesbeth
- Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Kerry Chester
- Department of Oncology, University College London, UCL Cancer Institute, 72 Huntley Street, London, WC1E 6BT, UK.
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10
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A direct qPCR method for residual DNA quantification in monoclonal antibody drugs produced in CHO cells. J Pharm Biomed Anal 2015; 115:603-6. [DOI: 10.1016/j.jpba.2015.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/03/2015] [Accepted: 03/05/2015] [Indexed: 01/21/2023]
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11
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Comparison of SYBR Green and TaqMan real-time PCR methods for quantitative detection of residual CHO host-cell DNA in biopharmaceuticals. Biologicals 2015; 43:130-5. [DOI: 10.1016/j.biologicals.2014.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 10/12/2014] [Accepted: 11/06/2014] [Indexed: 11/21/2022] Open
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12
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Peper G, Fankhauser A, Merlin T, Roscic A, Hofmann M, Obrdlik P. Direct real-time quantitative PCR for measurement of host-cell residual DNA in therapeutic proteins. J Pharm Biomed Anal 2014; 100:123-130. [PMID: 25151232 DOI: 10.1016/j.jpba.2014.07.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 11/29/2022]
Abstract
Real-time quantitative PCR (qPCR) is important for quantification of residual host cell DNA (resDNA) in therapeutic protein preparations. Typical qPCR protocols involve DNA extraction steps complicating sample handling. Here, we describe a "direct qPCR" approach without DNA extraction. To avoid interferences of DNA polymerase with a therapeutic protein, proteins in the samples were digested with proteinase K (PK) in the presence of sodium dodecyl sulfate (SDS). Tween 20 and NaCl were included to minimize precipitation of therapeutic proteins in the PK/SDS mix. After PK treatment, the solution was applied directly for qPCR. Inhibition of DNA polymerase by SDS was prevented by adding 2% (v/v) of Tween 20 to the final qPCR mix. The direct qPCR approach was evaluated for quantification of resDNA in therapeutic proteins manufactured in Chinese hamster ovary (CHO) host cells. First, direct qPCR was compared with qPCR applied on purified DNA ("extraction qPCR"). For both qPCRs, the same CHO-specific primers and probes were used. Comparable residual DNA levels were detected with both PCR approaches in purified and highly concentrated drug proteins as well as in in-process-control samples. Finally, the CHO-specific direct qPCR protocol was validated according to ICH guidelines and applied for 25 different therapeutic proteins. The specific limits of quantification were 0.1-0.8ppb for 24 proteins, and 2.0ppb for one protein. General applicability of the direct qPCR was demonstrated by applying the sample preparation protocol for quantification of resDNA in therapeutic proteins manufactured in other hosts such as Escherichia coli and mouse cells.
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Affiliation(s)
- Grit Peper
- Novartis Pharma AG, TRD Biologics Process R&D, Basel, Switzerland
| | | | - Thomas Merlin
- Novartis Pharma AG, TRD Biologics QC, Basel, Switzerland
| | - Ana Roscic
- Novartis Pharma AG, TRD Biologics Process R&D, Basel, Switzerland
| | - Matthias Hofmann
- Novartis Pharma AG, TRD Biologics Process R&D, Basel, Switzerland
| | - Petr Obrdlik
- Novartis Pharma AG, TRD Biologics Process R&D, Basel, Switzerland.
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13
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Farrell A, McLoughlin N, Milne JJ, Marison IW, Bones J. Application of Multi-Omics Techniques for Bioprocess Design and Optimization in Chinese Hamster Ovary Cells. J Proteome Res 2014; 13:3144-59. [DOI: 10.1021/pr500219b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amy Farrell
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Niaobh McLoughlin
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - John J. Milne
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Ian W. Marison
- Laboratory
of Integrated Bioprocessing, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Jonathan Bones
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
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14
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Chang JT, Chen YC, Chou YC, Wang SR. Quantitative detection of residual porcine host cell DNA by real-time PCR. Biologicals 2014; 42:74-8. [PMID: 24394374 DOI: 10.1016/j.biologicals.2013.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 03/12/2013] [Accepted: 10/24/2013] [Indexed: 11/17/2022] Open
Abstract
All biological products are derived from complex living systems and are often mixed with large numbers of impurities. For reasons of safety, residual host-cell DNA must be eliminated during processing. To assay host-cell DNA content in biopharmaceutical products derived from porcine sources, this study applies the quantitative real-time polymerase chain reaction (Q-PCR) method. The optimized assay in this study is based on the pol region of the porcine endogenous retrovirus (PERV). Assay validation results demonstrate that the proposed assay has appropriate accuracy, preciseness, reproducibility, and sensitivity. Primer and probe specificity are evaluated in real-time Q-PCR reactions using genomic DNA from rabbit, mouse, cat, hamster, monkey, human cell, yeast, and Escherichia coli as templates. The sensitivity of real-time Q-PCR is determined using genomic DNA from the porcine kidney cell line. The reliable detection range is within 0.5-10(5) pg/reaction. The limit of quantitation is 500 fg. The sensitivity of the assay meets the authority criterion. Moreover, the assay is applied to determine the level of host-cell DNA in recombinant human coagulation factor IX (rhFIX) from transgenic pigs. The real-time Q-PCR assay is thus a promising new tool for quantitative detection and clearance validation of residual porcine DNA when manufacturing recombinant therapeutics.
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Affiliation(s)
| | - Yu-Chen Chen
- Animal Technology Institute, Chunan, Miaoli, Taiwan
| | - Yu-Chi Chou
- Animal Technology Institute, Chunan, Miaoli, Taiwan
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15
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Chen Z, He Y, Shi B, Yang D. Human serum albumin from recombinant DNA technology: Challenges and strategies. Biochim Biophys Acta Gen Subj 2013; 1830:5515-25. [DOI: 10.1016/j.bbagen.2013.04.037] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/24/2013] [Accepted: 04/29/2013] [Indexed: 12/22/2022]
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16
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Wang L, Rao C, Gao K, Li Y, Fu Z, Bi H, Wang J. Development of a reference standard of Escherichia coli DNA for residual DNA determination in China. PLoS One 2013; 8:e74166. [PMID: 24086318 PMCID: PMC3783418 DOI: 10.1371/journal.pone.0074166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 07/26/2013] [Indexed: 11/30/2022] Open
Abstract
This collaborative study developed the first national Escherichia coli (E. coli) DNA reference standard for standardizing quantitative residual DNA assay methods, fluorescence dye (PicoGreen) and quantitative PCR (q-PCR), which were widely employed to measure residual DNA contents of prokaryotic-derived recombinant products. High purity of E. coli strain BL21 was extracted by the cetyl triethyl ammonium bromide (CTAB)/phenol chloroform method, analyzed by UV-visible spectrophotometry and electrophoresis, diluted with tris-EDTA (TE) buffer and manually dispensed. Then, with a cooperative calibration among six laboratories, including five manufacturers and one national control laboratory, the concentration of E. coli DNA standard solution was determined as 96.2 μg/mL (95% C.I: 95.5–96.9 μg/mL, CV 3.4%). The candidate showed excellent stability both from accelerated degradation study and real time stability study. The applicability study showed that the E. coli DNA reference could reach the sensitivity of 0.781 ng/mL and 1 fg/μL, respectively, in fluorescent dye and q-PCR assay, and also had good linearity and precision. The consistency of the reference could meet the requirements of the national reference standard. As a conclusion, the candidate material was suitable to serve as a China national standard for E. coli residual DNA determination. The successful establishment of the E. coli DNA standard will facilitate the standardization of quantitative methods for testing residual host cell DNA.
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Affiliation(s)
- Lan Wang
- National Institutes of Food and Drug Control, Beijing, People's Republic of China
| | - Chunming Rao
- National Institutes of Food and Drug Control, Beijing, People's Republic of China
| | - Kai Gao
- National Institutes of Food and Drug Control, Beijing, People's Republic of China
| | - Yonghong Li
- National Institutes of Food and Drug Control, Beijing, People's Republic of China
| | - Zhihao Fu
- National Institutes of Food and Drug Control, Beijing, People's Republic of China
| | - Hua Bi
- National Institutes of Food and Drug Control, Beijing, People's Republic of China
| | - Junzhi Wang
- National Institutes of Food and Drug Control, Beijing, People's Republic of China
- * E-mail:
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17
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Sedlackova T, Repiska G, Celec P, Szemes T, Minarik G. Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods. Biol Proced Online 2013; 15:5. [PMID: 23406353 PMCID: PMC3576356 DOI: 10.1186/1480-9222-15-5] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/09/2013] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED BACKGROUND Specific applications and modern technologies, like non-invasive prenatal testing, non-invasive cancer diagnostic and next generation sequencing, are currently in the focus of researchers worldwide. These have common characteristics in use of highly fragmented DNA molecules for analysis. Hence, for the performance of molecular methods, DNA concentration is a crucial parameter; we compared the influence of different levels of DNA fragmentation on the accuracy of DNA concentration measurements. RESULTS In our comparison, the performance of the currently most commonly used methods for DNA concentration measurement (spectrophotometric, fluorometric and qPCR based) were tested on artificially fragmented DNA samples. In our comparison, unfragmented and three specifically fragmented DNA samples were used.According to our results, the level of fragmentation did not influence the accuracy of spectrophotometric measurements of DNA concentration, while other methods, fluorometric as well as qPCR-based, were significantly influenced and a decrease in measured concentration was observed with more intensive DNA fragmentation. CONCLUSIONS Our study has confirmed that the level of fragmentation of DNA has significant impact on accuracy of DNA concentration measurement with two of three mostly used methods (PicoGreen and qPCR). Only spectrophotometric measurement was not influenced by the level of fragmentation, but sensitivity of this method was lowest among the three tested. Therefore if it is possible the DNA quantification should be performed with use of equally fragmented control DNA.
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Affiliation(s)
- Tatiana Sedlackova
- Institute of Molecular BioMedicine, Faculty of Medicine, Comenius University, Sasinkova 4, Bratislava, 811 08, Slovakia.
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18
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Borlido L, Azevedo A, Sousa A, Oliveira P, Roque A, Aires-Barros M. Fishing human monoclonal antibodies from a CHO cell supernatant with boronic acid magnetic particles. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 903:163-70. [DOI: 10.1016/j.jchromb.2012.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/12/2012] [Accepted: 07/15/2012] [Indexed: 10/28/2022]
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Kang MJ, Yu H, Kim SK, Park SR, Yang I. Quantification of trace-level DNA by real-time whole genome amplification. PLoS One 2011; 6:e28661. [PMID: 22174862 PMCID: PMC3235147 DOI: 10.1371/journal.pone.0028661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 11/12/2011] [Indexed: 11/18/2022] Open
Abstract
Quantification of trace amounts of DNA is a challenge in analytical applications where the concentration of a target DNA is very low or only limited amounts of samples are available for analysis. PCR-based methods including real-time PCR are highly sensitive and widely used for quantification of low-level DNA samples. However, ordinary PCR methods require at least one copy of a specific gene sequence for amplification and may not work for a sub-genomic amount of DNA. We suggest a real-time whole genome amplification method adopting the degenerate oligonucleotide primed PCR (DOP-PCR) for quantification of sub-genomic amounts of DNA. This approach enabled quantification of sub-picogram amounts of DNA independently of their sequences. When the method was applied to the human placental DNA of which amount was accurately determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES), an accurate and stable quantification capability for DNA samples ranging from 80 fg to 8 ng was obtained. In blind tests of laboratory-prepared DNA samples, measurement accuracies of 7.4%, -2.1%, and -13.9% with analytical precisions around 15% were achieved for 400-pg, 4-pg, and 400-fg DNA samples, respectively. A similar quantification capability was also observed for other DNA species from calf, E. coli, and lambda phage. Therefore, when provided with an appropriate standard DNA, the suggested real-time DOP-PCR method can be used as a universal method for quantification of trace amounts of DNA.
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Affiliation(s)
- Min-Jung Kang
- Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejon, Republic of Korea
| | - Hannah Yu
- Department of Bio-Analytical Science, University of Science and Technology, Daejon, Republic of Korea
| | - Sook-Kyung Kim
- Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejon, Republic of Korea
| | - Sang-Ryoul Park
- Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejon, Republic of Korea
| | - Inchul Yang
- Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejon, Republic of Korea
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Verardo ML, Carvalho JG, Delgado DN, Kuhns ST. Accuracy and sensitivity of residual DNA detection by QPCR is not predicted by target copy number. Biotechnol Prog 2011; 28:428-34. [PMID: 22095674 DOI: 10.1002/btpr.731] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 09/12/2011] [Indexed: 01/25/2023]
Abstract
A major issue in the use of mammalian cell culture in biopharmaceutical manufacturing is the removal of process related impurities, such as residual host cell DNA, during the product purification process. To ensure that sufficient DNA removal is achieved during purification, it is essential to have an accurate and sensitive assay for host cell DNA. The quantitative polymerase chain reaction (QPCR) is widely used for this purpose; however, the extent to which the choice of QPCR gene target can have an impact on final results requires further understanding. In the present study, we examined the relationship between the genomic copy number of eight different Chinese Hamster ovary (CHO) gene targets and the sensitivity and accuracy afforded by those targets in a residual host cell DNA QPCR assay. We also evaluated the use of each gene target for accurate measurement of residual DNA clearance using in-process purification samples from two CHO production cell lines. Our results revealed a correlation between gene target abundance and the potential sensitivity for use in a QPCR assay. However, we found that higher copy number gene targets do not provide the highest measurement or reveal the largest clearance of residual host cell DNA from purification samples. These findings suggest that different DNA sequences may clear or degrade at differential rates and highlight unexpected considerations that must be made in the choice of QPCR gene target when designing QPCR assays.
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Affiliation(s)
- Megan L Verardo
- Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA
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Druz A, Chu C, Majors B, Santuary R, Betenbaugh M, Shiloach J. A novel microRNA mmu-miR-466h affects apoptosis regulation in mammalian cells. Biotechnol Bioeng 2011; 108:1651-61. [PMID: 21337326 DOI: 10.1002/bit.23092] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/11/2011] [Accepted: 02/02/2011] [Indexed: 12/15/2022]
Abstract
This study determined the changes in microRNA (miRs) expression in mammalian Chinese hamster ovary (CHO) cells undergoing apoptosis induced by exposing the cells to nutrient-depleted media. The apoptosis onset was confirmed by reduced cell viability and Caspase-3/7 activation. Microarray comparison of known mouse and rat miRs in CHO cells exposed to fresh or depleted media revealed up-regulation of the mouse miR-297-669 cluster in CHO cells subjected to depleted media. The mmu-miR-466h was chosen for further analysis as the member of this cluster with the highest overexpression and its up-regulation in depleted media was confirmed with qRT-PCR. Since miRs suppress mRNA translation, we hypothesized that up-regulated mmu-miR-466h inhibits anti-apoptotic genes and induces apoptosis. A combination of bioinformatics and experimental tools was used to predict and verify mmu-miR-466h anti-apoptotic targets. 8708 predicted targets were obtained from miRecords database and narrowed to 38 anti-apoptotic genes with DAVID NCBI annotation tool. Several genes were selected from this anti-apoptotic subset based on nucleotide pairing complimentarity between the mmu-miR-466h seed region and 3' UTR of the target mRNAs. The qRT-PCR analysis revealed reduced mRNA levels of bcl2l2, dad1, birc6, stat5a, and smo genes in CHO cells exposed to depleted media. The inhibition of the mmu-miR-466h increased the expression levels of those genes and resulted in increased cell viability and decreased Caspase-3/7 activation. The up-regulation of mmu-miR-466h in response to nutrients depletion causes the inhibition of several anti-apoptotic genes in unison. This suggests the pro-apoptotic role of mmu-miR-466h and its capability to modulate the apoptotic pathway in mammalian cells.
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Affiliation(s)
- Aliaksandr Druz
- Biotechnology Core Laboratory National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike Bldg 14A Rm 176, Bethesda, Maryland 20892, USA
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22
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Development and characterization of a novel host cell DNA assay using ultra-sensitive fluorescent nucleic acid stain “PicoGreen”. J Pharm Biomed Anal 2009; 49:997-1002. [DOI: 10.1016/j.jpba.2009.01.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 01/09/2009] [Accepted: 01/16/2009] [Indexed: 11/20/2022]
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