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Andrew LJ, Kly S, Moloney EG, Moffitt MG. Effects of Microfluidic Shear on the Plasmid DNA Structure: Implications for Polymeric Gene Delivery Vectors. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11545-11555. [PMID: 37552625 DOI: 10.1021/acs.langmuir.3c00934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Microfluidic manufacturing of advanced gene delivery vectors necessitates consideration of the effects of microfluidic shear forces on the structural integrity of plasmid DNA (pDNA). In this paper, we expose pDNA to variable shear forces in a two-phase, gas-liquid microfluidic reactor and apply gel electrophoresis to analyze the products of on-chip shear-induced degradation. The effects of shear rate, solvent environment, pDNA size, and copolymer complexation on shear-induced degradation are investigated. We find that small naked pDNA (pUC18, 2.7 kb) exhibits shear rate-dependent shear degradation in the microfluidic channels in a mixed organic solvent (dioxane/water/acetic acid; 90/10/<0.1 w/w/w), with the extents of both supercoil isoform relaxation and complete fragmentation increasing as the maximum shear rates increase from 4 × 105 to 2 × 106 s-1. However, over the same range of shear rates, the same pDNA sample shows no evidence of microfluidic shear-induced degradation in a pure aqueous environment. Quiescent control experiments in the same mixed organic solvent prove that a combination of solvent and shear forces is involved in the observed shear-induced degradation. Furthermore, we show that shear degradation effects in mixed organic solvents can be significantly attenuated by complexation of pDNA with the block copolymer polycaprolactone-block-poly(2-vinylpyridine) prior to exposure to microfluidic shear. Finally, we demonstrate that medium (pDSK519, 8.1 kb) and large (pRK290, 20 kb) naked pDNA are more sensitive to shear-induced microfluidic degradation in the mixed organic solvent environment than small pDNA, with both plasmids showing complete fragmentation even at the lowest shear rate, although we found no evidence of shear-induced damage in water for the largest investigated naked pDNA even at the highest flow rate. The resulting understanding of the interplay of the solvent and shear effects during microfluidic processing should inform microfluidic manufacturing routes to new gene therapy formulations.
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Affiliation(s)
- Lucas J Andrew
- Department of Chemistry, University of Victoria, P.O. Box 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada
| | - Sundiata Kly
- Department of Chemistry, University of Victoria, P.O. Box 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada
| | - Erin G Moloney
- Department of Chemistry, University of Victoria, P.O. Box 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada
| | - Matthew G Moffitt
- Department of Chemistry, University of Victoria, P.O. Box 1700 Stn CSC, Victoria, BC V8W 2Y2, Canada
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Effects of varying flux and transmembrane pressure conditions during ceramic ultrafiltration on the infectivity and retention of MS2 bacteriophages. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Schwaller C, Fokkens K, Helmreich B, Drewes JE. CFD simulations of flow fields during ultrafiltration: Effects of hydrodynamic strain rates with and without a particle cake layer on the permeation of mobile genetic elements. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.117606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
Relative to other extrinsic factors, the effects of hydrodynamic flow fields on protein stability and conformation remain poorly understood. Flow-induced protein remodeling and/or aggregation is observed both in Nature and during the large-scale industrial manufacture of proteins. Despite its ubiquity, the relationships between the type and magnitude of hydrodynamic flow, a protein's structure and stability, and the resultant aggregation propensity are unclear. Here, we assess the effects of a defined and quantified flow field dominated by extensional flow on the aggregation of BSA, β2-microglobulin (β2m), granulocyte colony stimulating factor (G-CSF), and three monoclonal antibodies (mAbs). We show that the device induces protein aggregation after exposure to an extensional flow field for 0.36-1.8 ms, at concentrations as low as 0.5 mg mL-1 In addition, we reveal that the extent of aggregation depends on the applied strain rate and the concentration, structural scaffold, and sequence of the protein. Finally we demonstrate the in situ labeling of a buried cysteine residue in BSA during extensional stress. Together, these data indicate that an extensional flow readily unfolds thermodynamically and kinetically stable proteins, exposing previously sequestered sequences whose aggregation propensity determines the probability and extent of aggregation.
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Critical considerations for developing nucleic acid macromolecule based drug products. Drug Discov Today 2015; 21:430-44. [PMID: 26674130 DOI: 10.1016/j.drudis.2015.11.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 11/02/2015] [Accepted: 11/25/2015] [Indexed: 01/02/2023]
Abstract
Protein expression therapy using nucleic acid macromolecules (NAMs) as a new paradigm in medicine has recently gained immense therapeutic potential. With the advancement of nonviral delivery it has been possible to target NAMs against cancer, immunodeficiency and infectious diseases. Owing to the complex and fragile structure of NAMs, however, development of a suitable, stable formulation for a reasonable product shelf-life and efficacious delivery is indeed challenging to achieve. This review provides a synopsis of challenges in the formulation and stability of DNA/m-RNA based medicines and probable mitigation strategies including a brief summary of delivery options to the target cells. Nucleic acid based drugs at various stages of ongoing clinical trials are compiled.
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Nesterova IV, Hupert ML, Witek MA, Soper SA. Hydrodynamic shearing of DNA in a polymeric microfluidic device. LAB ON A CHIP 2012; 12:1044-1047. [PMID: 22314498 DOI: 10.1039/c2lc21122j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
With the advent of next-generation sequencing (NGS) systems and the associated high throughput they afford, the input to these machines requires manageable lengths of fragments (~1000 bp) produced from chromosomal DNAs. Therefore, it is critical to develop devices that can shear DNA in a controlled fashion. We report a polymer-based microfluidic device that establishes an efficient and inexpensive platform with performance comparable to a commercially available bench-top system.
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Affiliation(s)
- Irina V Nesterova
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70820, USA
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Ongkudon CM, Pickering R, Webster D, Danquah MK. Cultivation of E. coli carrying a plasmid-based Measles vaccine construct (4.2 kbp pcDNA3F) employing medium optimisation and pH-temperature induction techniques. Microb Cell Fact 2011; 10:16. [PMID: 21375765 PMCID: PMC3059270 DOI: 10.1186/1475-2859-10-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 03/05/2011] [Indexed: 11/10/2022] Open
Abstract
Background Plasmid-based measles vaccines offer great promises over the conventional fertilised egg method such as ease of manufacture and mimic wild-type intracellular antigen expression. The increasing number of clinical trials on plasmid-based measles vaccines has triggered the need to make more in less time. Results In this work, we investigated the process variables necessary to improve the volumetric and specific yields of a model plasmid-based measles vaccine (pcDNA3F) harboured in E. coli DH5α. Results from growth medium optimisation in 500 mL shake flasks by response surface methodology (RSM) generated a maximum volumetric yield of 13.65 mg/L which was 1.75 folds higher than that of the base medium. A controlled fed-batch fermentation employing strategic glycerol feeding and optimised growth conditions resulted in a remarkable pcDNA3F volumetric yield of 110 mg/L and a specific yield of 14 mg/g. In addition, growth pH modification and temperature fluctuation between 35 and 45°C were successfully employed to improve plasmid production. Conclusion Production of a high copy number plasmid DNA containing a foreign gene of interest is often hampered by the low plasmid volumetric yield which results from the over expression of foreign proteins and metabolic repressors. In this work, a simple bioprocess framework was employed and successfully improved the production of pcDNA3F.
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Affiliation(s)
- Clarence M Ongkudon
- Bio Engineering Laboratory, Department of Chemical Engineering, Monash University, Clayton campus, Wellington road, Victoria 3800, Australia.
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Ongkudon CM, Ho J, Danquah MK. Mitigating the looming vaccine crisis: production and delivery of plasmid-based vaccines. Crit Rev Biotechnol 2010; 31:32-52. [DOI: 10.3109/07388551.2010.483460] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Bee JS, Stevenson JL, Mehta B, Svitel J, Pollastrini J, Platz R, Freund E, Carpenter JF, Randolph TW. Response of a concentrated monoclonal antibody formulation to high shear. Biotechnol Bioeng 2009; 103:936-43. [PMID: 19370772 PMCID: PMC2724069 DOI: 10.1002/bit.22336] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
There is concern that shear could cause protein unfolding or aggregation during commercial biopharmaceutical production. In this work we exposed two concentrated immunoglobulin-G1 (IgG1) monoclonal antibody (mAb, at >100 mg/mL) formulations to shear rates between 20,000 and 250,000 s(-1) for between 5 min and 30 ms using a parallel-plate and capillary rheometer, respectively. The maximum shear and force exposures were far in excess of those expected during normal processing operations (20,000 s(-1) and 0.06 pN, respectively). We used multiple characterization techniques to determine if there was any detectable aggregation. We found that shear alone did not cause aggregation, but that prolonged exposure to shear in the stainless steel parallel-plate rheometer caused a very minor reversible aggregation (<0.3%). Additionally, shear did not alter aggregate populations in formulations containing 17% preformed heat-induced aggregates of a mAb. We calculate that the forces applied to a protein by production shear exposures (<0.06 pN) are small when compared with the 140 pN force expected at the air-water interface or the 20-150 pN forces required to mechanically unfold proteins described in the atomic force microscope (AFM) literature. Therefore, we suggest that in many cases, air-bubble entrainment, adsorption to solid surfaces (with possible shear synergy), contamination by particulates, or pump cavitation stresses could be much more important causes of aggregation than shear exposure during production.
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Affiliation(s)
- Jared S. Bee
- University of Colorado, Department of Chemical and Biological Engineering, Room: ECCH 111, Campus Box 0424, 1111 Engineers Dr, Boulder, Colorado 80309-0424, Telephone: 303-492-4776
| | | | - Bhavya Mehta
- Drug Product & Device Development, Amgen Inc., Thousand Oaks, CA 91320
| | - Juraj Svitel
- Formulation and Analytical Resources, Amgen Inc., Thousand Oaks, CA 91320
| | - Joey Pollastrini
- Formulation and Analytical Resources, Amgen Inc., Thousand Oaks, CA 91320
| | | | - Erwin Freund
- Drug Product & Device Development, Amgen Inc., Thousand Oaks, CA 91320
| | - John F. Carpenter
- Department of Pharmaceutical Sciences, University of Colorado Health Sciences Center, Denver, Colorado 80262
| | - Theodore W. Randolph
- University of Colorado, Department of Chemical and Biological Engineering, Room: ECCH 111, Campus Box 0424, 1111 Engineers Dr, Boulder, Colorado 80309-0424, Telephone: 303-492-4776
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Generation of chromosomal DNA during alkaline lysis and removal by reverse micellar extraction. Appl Microbiol Biotechnol 2009; 84:199-204. [DOI: 10.1007/s00253-009-2088-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 06/09/2009] [Accepted: 06/09/2009] [Indexed: 11/25/2022]
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Titchener-Hooker NJ, Dunnill P, Hoare M. Micro biochemical engineering to accelerate the design of industrial-scale downstream processes for biopharmaceutical proteins. Biotechnol Bioeng 2008; 100:473-87. [PMID: 18438873 DOI: 10.1002/bit.21788] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- N J Titchener-Hooker
- Department of Biochemical Engineering, Advanced Centre for Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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Zhang H, Kong S, Booth A, Boushaba R, Levy MS, Hoare M. Prediction of Shear Damage of Plasmid DNA in Pump and Centrifuge Operations Using an Ultra Scale-Down Device. Biotechnol Prog 2007. [DOI: 10.1002/bp070066z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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