1
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Rohskopf Z, Kwon T, Ko SH, Bozinovski D, Jeon H, Mohan N, Springs SL, Han J. Continuous Online Titer Monitoring in CHO Cell Culture Supernatant Using a Herringbone Nanofluidic Filter Array. Anal Chem 2023; 95:14608-14615. [PMID: 37733929 DOI: 10.1021/acs.analchem.3c02104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Online monitoring of monoclonal antibody product titers throughout biologics process development and production enables rapid bioprocess decision-making and process optimization. Conventional analytical methods, including high-performance liquid chromatography and turbidimetry, typically require interfacing with an automated sampling system capable of online sampling and fractionation, which suffers from increased cost, a higher risk of failure, and a higher mechanical complexity of the system. In this study, a novel nanofluidic system for continuous direct (no sample preparation) IgG titer measurements was investigated. Tumor necrosis factor α (TNF-α), conjugated with fluorophores, was utilized as a selective binder for adalimumab in the unprocessed cell culture supernatant. The nanofluidic device can separate the bound complex from unbound TNF-α and selectively concentrate the bound complex for high-sensitivity detection. Based on the fluorescence intensity from the concentrated bound complex, a fluorescence intensity versus titer curve can be generated, which was used to determine the titer of samples from filtered, unpurified Chinese hamster ovary cell cultures continuously. The system performed direct monitoring of IgG titers with nanomolar resolution and showed a good correlation with the biolayer interferometry assays. Furthermore, by variation of the concentration of the indicator (TNF-α), the dynamic range of the system can be tuned and further expanded.
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Affiliation(s)
- Zhumei Rohskopf
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Taehong Kwon
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge,Massachusetts 02139, United States
| | - Sung Hee Ko
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge,Massachusetts 02139, United States
| | - Dragana Bozinovski
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyungkook Jeon
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Naresh Mohan
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Critical Analytics for Manufacturing Personalized-Medicine (CAMP) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore117583,Singapore
| | - Jongyoon Han
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge,Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Critical Analytics for Manufacturing Personalized-Medicine (CAMP) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore117583,Singapore
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2
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Destro F, Joseph J, Srinivasan P, Kanter JM, Neufeld C, Wolfrum JM, Barone PW, Springs SL, Sinskey AJ, Cecchini S, Kotin RM, Braatz RD. Mechanistic modeling explains the production dynamics of recombinant adeno-associated virus with the baculovirus expression vector system. Mol Ther Methods Clin Dev 2023; 30:122-146. [PMID: 37746245 PMCID: PMC10512016 DOI: 10.1016/j.omtm.2023.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/30/2023] [Indexed: 09/26/2023]
Abstract
Current manufacturing processes for recombinant adeno-associated viruses (rAAVs) have less-than-desired yields and produce significant amounts of empty capsids. The increasing demand and the high cost of goods for rAAV-based gene therapies motivate development of more efficient manufacturing processes. Recently, the US Food and Drug Administration (FDA) approved the first rAAV-based gene therapy product manufactured in the baculovirus expression vector system (BEVS), a technology that demonstrated production of high titers of full capsids. This work presents a first mechanistic model describing the key extracellular and intracellular phenomena occurring during baculovirus infection and rAAV maturation in the BEVS. The model predictions are successfully validated for in-house and literature experimental measurements of the vector genome and of structural and non-structural proteins collected during rAAV manufacturing in the BEVS with the TwoBac and ThreeBac constructs. A model-based analysis of the process is carried out to identify the bottlenecks that limit full capsid formation. Vector genome amplification is found to be the limiting step for rAAV production in Sf9 cells using either the TwoBac or ThreeBac system. In turn, vector genome amplification is hindered by limiting Rep78 levels. Transgene and non-essential baculovirus protein expression in the insect cell during rAAV manufacturing also negatively influences the rAAV production yields.
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Affiliation(s)
- Francesco Destro
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John Joseph
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Prasanna Srinivasan
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joshua M. Kanter
- Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Caleb Neufeld
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jacqueline M. Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Paul W. Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stacy L. Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony J. Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sylvain Cecchini
- Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Robert M. Kotin
- Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Carbon Biosciences, Waltham, MA 02451, USA
| | - Richard D. Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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3
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Strutt JPB, Natarajan M, Lee E, Teo DBL, Sin WX, Cheung KW, Chew M, Thazin K, Barone PW, Wolfrum JM, Williams RBH, Rice SA, Springs SL. Machine learning-based detection of adventitious microbes in T-cell therapy cultures using long-read sequencing. Microbiol Spectr 2023; 11:e0135023. [PMID: 37646508 PMCID: PMC10580871 DOI: 10.1128/spectrum.01350-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 09/01/2023] Open
Abstract
Assuring that cell therapy products are safe before releasing them for use in patients is critical. Currently, compendial sterility testing for bacteria and fungi can take 7-14 days. The goal of this work was to develop a rapid untargeted approach for the sensitive detection of microbial contaminants at low abundance from low volume samples during the manufacturing process of cell therapies. We developed a long-read sequencing methodology using Oxford Nanopore Technologies MinION platform with 16S and 18S amplicon sequencing to detect USP <71> organisms and other microbial species. Reads are classified metagenomically to predict the microbial species. We used an extreme gradient boosting machine learning algorithm (XGBoost) to first assess if a sample is contaminated, and second, determine whether the predicted contaminant is correctly classified or misclassified. The model was used to make a final decision on the sterility status of the input sample. An optimized experimental and bioinformatics pipeline starting from spiked species through to sequenced reads allowed for the detection of microbial samples at 10 colony-forming units (CFU)/mL using metagenomic classification. Machine learning can be coupled with long-read sequencing to detect and identify sample sterility status and microbial species present in T-cell cultures, including the USP <71> organisms to 10 CFU/mL. IMPORTANCE This research presents a novel method for rapidly and accurately detecting microbial contaminants in cell therapy products, which is essential for ensuring patient safety. Traditional testing methods are time-consuming, taking 7-14 days, while our approach can significantly reduce this time. By combining advanced long-read nanopore sequencing techniques and machine learning, we can effectively identify the presence and types of microbial contaminants at low abundance levels. This breakthrough has the potential to improve the safety and efficiency of cell therapy manufacturing, leading to better patient outcomes and a more streamlined production process.
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Affiliation(s)
- James P. B. Strutt
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | | | - Elizabeth Lee
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Denise Bei Lin Teo
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Wei-Xiang Sin
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Ka-Wai Cheung
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Marvin Chew
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Khaing Thazin
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Paul W. Barone
- MIT Center for Biomedical Innovation, Massachusetts Institute of Technology, Boston, USA
| | - Jacqueline M. Wolfrum
- MIT Center for Biomedical Innovation, Massachusetts Institute of Technology, Boston, USA
| | - Rohan B. H. Williams
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- CSIRO Microbiomes for One Systems Health, Agriculture and Food, Westmead, Australia
| | - Stacy L. Springs
- Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
- MIT Center for Biomedical Innovation, Massachusetts Institute of Technology, Boston, USA
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4
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Barone PW, Keumurian FJ, Neufeld C, Koenigsberg A, Kiss R, Leung J, Wiebe M, Ait-Belkacem R, Azimpour Tabrizi C, Barbirato C, Beurdeley P, Brussel A, Cassart JP, Cote C, Deneyer N, Dheenadhayalan V, Diaz L, Geiselhoeringer A, Gilleece MM, Goldmann J, Hickman D, Holden A, Keiner B, Kopp M, Kreil TR, Lambert C, Logvinoff C, Michaels B, Modrof J, Mullan B, Mullberg J, Murphy M, O'Donnell S, Peña J, Ruffing M, Ruppach H, Salehi N, Shaid S, Silva L, Snyder R, Spedito-Jovial M, Vandeputte O, Westrek B, Yang B, Yang P, Springs SL. Historical evaluation of the in vivo adventitious virus test and its potential for replacement with next generation sequencing (NGS). Biologicals 2023; 81:101661. [PMID: 36621353 DOI: 10.1016/j.biologicals.2022.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/29/2022] [Indexed: 01/09/2023] Open
Abstract
The Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) collected historical data from 20 biopharmaceutical industry members on their experience with the in vivo adventitious virus test, the in vitro virus test, and the use of next generation sequencing (NGS) for viral safety. Over the past 20 years, only three positive in vivo adventitious virus test results were reported, and all were also detected in another concurrent assay. In more than three cases, data collected as a part of this study also found that the in vivo adventitious virus test had given a negative result for a sample that was later found to contain virus. Additionally, the in vivo adventitious virus test had experienced at least 21 false positives and had to be repeated an additional 21 times all while using more than 84,000 animals. These data support the consideration and need for alternative broad spectrum viral detection tests that are faster, more sensitive, more accurate, more specific, and more humane. NGS is one technology that may meet this need. Eighty one percent of survey respondents are either already actively using or exploring the use of NGS for viral safety. The risks and challenges of replacing in vivo adventitious virus testing with NGS are discussed. It is proposed to update the overall virus safety program for new biopharmaceutical products by replacing in vivo adventitious virus testing approaches with modern methodologies, such as NGS, that maintain or even improve the final safety of the product.
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Affiliation(s)
| | | | | | | | - Robert Kiss
- MIT Center for Biomedical Innovation, USA; UPSIDE Foods, USA
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5
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Swofford CA, Nordeen SA, Chen L, Desai MM, Chen J, Springs SL, Schwartz TU, Sinskey AJ. Structure and Specificity of an Anti-Chloramphenicol Single Domain Antibody for Detection of Amphenicol Residues. Protein Sci 2022; 31:e4457. [PMID: 36153664 PMCID: PMC9601811 DOI: 10.1002/pro.4457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/31/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022]
Abstract
Antibiotics in aquaculture prevent bacterial infection of fish, but their misuse is a public health risk and contributes to the unintentional creation of multiresistant pathogens. Regulatory agencies cannot do the rigorous, expensive testing required to keep up with the volume of seafood shipments. Current rapid test kits for these drugs enable the increase in testing needed for adequate monitoring of food supply chains, but they lack a high degree of accuracy. To combat this, we set out to discover and engineer single‐domain antibodies (VHHs) that bind to small molecule antibiotics, and that can be used in rapid test kits. The small size, solubility, and stability of VHHs are useful properties that can improve the reliability and shelf‐life of test kits for these adulterants. Here, we report a novel anti‐chloramphenicol VHH (Chl‐VHH) with a disassociation constant of 57 nM. This was achieved by immunizing a llama against a chloramphenicol‐keyhole limpet hemocyanin (KLH) conjugate and screening for high affinity binders through phage display. The crystal structure of the bound‐VHH to chloramphenicol was key to identifying a mutation in the binding pocket that resulted in a 16‐fold improvement in binding affinity. In addition, the structure provides new insights into VHH‐hapten interactions that can guide future engineering of VHHs against additional targets. PDB Code(s): 7TJC;
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Affiliation(s)
- Charles A Swofford
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA.,Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA
| | - Sarah A Nordeen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Lu Chen
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA
| | - Mahaam M Desai
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA
| | - Joanna Chen
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA.,Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA
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6
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Wu X, Chan C, Springs SL, Lee YH, Lu TK, Yu H. A warm-start digital CRISPR/Cas-based method for the quantitative detection of nucleic acids. Anal Chim Acta 2022; 1196:339494. [DOI: 10.1016/j.aca.2022.339494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/03/2022] [Accepted: 01/11/2022] [Indexed: 12/21/2022]
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7
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Katsikis G, Hwang IE, Wang W, Bhat VS, McIntosh NL, Karim OA, Blus BJ, Sha S, Agache V, Wolfrum JM, Springs SL, Sinskey AJ, Barone PW, Braatz RD, Manalis SR. Weighing the DNA Content of Adeno-Associated Virus Vectors with Zeptogram Precision Using Nanomechanical Resonators. Nano Lett 2022; 22:1511-1517. [PMID: 35148107 DOI: 10.1021/acs.nanolett.1c04092] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Quantifying the composition of viral vectors used in vaccine development and gene therapy is critical for assessing their functionality. Adeno-associated virus (AAV) vectors, which are the most widely used viral vectors for in vivo gene therapy, are typically characterized using PCR, ELISA, and analytical ultracentrifugation which require laborious protocols or hours of turnaround time. Emerging methods such as charge-detection mass spectroscopy, static light scattering, and mass photometry offer turnaround times of minutes for measuring AAV mass using optical or charge properties of AAV. Here, we demonstrate an orthogonal method where suspended nanomechanical resonators (SNR) are used to directly measure both AAV mass and aggregation from a few microliters of sample within minutes. We achieve a precision near 10 zeptograms which corresponds to 1% of the genome holding capacity of the AAV capsid. Our results show the potential of our method for providing real-time quality control of viral vectors during biomanufacturing.
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Affiliation(s)
- Georgios Katsikis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Iris E Hwang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wade Wang
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Vikas S Bhat
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Nicole L McIntosh
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Omair A Karim
- BioMarin Pharmaceutical, Inc., Novato, California 94949, United States
| | - Bartlomiej J Blus
- BioMarin Pharmaceutical, Inc., San Rafael, California 94901, United States
| | - Sha Sha
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vincent Agache
- Université Grenoble Alpes, CEA, LETI, 38000, Grenoble, France
| | - Jacqueline M Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony J Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Richard D Braatz
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Chen L, Guttieres D, Koenigsberg A, Barone PW, Sinskey AJ, Springs SL. Large-scale cultured meat production: Trends, challenges and promising biomanufacturing technologies. Biomaterials 2021; 280:121274. [PMID: 34871881 DOI: 10.1016/j.biomaterials.2021.121274] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023]
Abstract
Food systems of the future will need to face an increasingly clear reality - that a protein-rich diet is essential for good health, but traditional meat products will not suffice to ensure safety, sustainability, and equity of food supply chains at a global scale. This paper provides an in-depth analysis of bioprocess technologies needed for cell-based meat production and challenges in reaching commercial scale. Specifically, it reviews state-of-the-art bioprocess technologies, current limitations, and opportunities for research across four domains: cell line development, cell culture media, scaffolding, and bioreactors. This also includes exploring innovations to make cultured meat a viable protein alternative across numerous key performance indicators and for specific applications where traditional livestock is not an option (e.g., local production, space exploration). The paper explores tradeoffs between production scale, product quality, production cost, and footprint over different time horizons. Finally, a discussion explores various factors that may impact the ability to successfully scale and market cultured meat products: social acceptance, environmental tradeoffs, regulatory guidance, and public health benefits. While the exact nature of the transition from traditional livestock to alternative protein products is uncertain, it has already started and will likely continue to build momentum in the next decade.
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Affiliation(s)
- Lu Chen
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Donovan Guttieres
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Andrea Koenigsberg
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Paul W Barone
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Anthony J Sinskey
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States
| | - Stacy L Springs
- Massachusetts Institute of Technology, Center for Biomedical Innovation, Cambridge, MA, United States.
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9
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Hong MS, Lu AE, Ou RW, Wolfrum JM, Springs SL, Sinskey AJ, Braatz RD. Model-based control for column-based continuous viral inactivation of biopharmaceuticals. Biotechnol Bioeng 2021; 118:3215-3224. [PMID: 34101159 DOI: 10.1002/bit.27846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/15/2021] [Accepted: 05/30/2021] [Indexed: 11/08/2022]
Abstract
Batch low-pH hold is a common processing step to inactivate enveloped viruses for biologics derived from mammalian sources. Increased interest in the transition of biopharmaceutical manufacturing from batch to continuous operation resulted in numerous attempts to adapt batch low-pH hold to continuous processing. However, control challenges with operating this system have not been directly addressed. This article describes a low-cost, column-based continuous viral inactivation system constructed with off-the-shelf components. Model-based, reaction-invariant pH controller is implemented to account for the nonlinearities with Bayesian estimation addressing variations in the operation. The residence time distribution is modeled as a plug flow reactor with axial dispersion in series with a continuously stirred tank reactor, and is periodically estimated during operation through inverse tracer experiments. The estimated residence time distribution quantifies the minimum residence time, which is used to adjust feed flow rates. Controller validation experiments demonstrate that pH and minimum residence time setpoint tracking and disturbance rejection are achieved with fast and accurate response and no instability. Viral inactivation testing demonstrates tight control of logarithmic reduction values over extended operation. This study provides tools for the design and operation of continuous viral inactivation systems in service of increasing productivity, improving product quality, and enhancing patient safety.
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Affiliation(s)
- Moo Sun Hong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amos E Lu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rui Wen Ou
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jacqueline M Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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10
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Nguyen TN, Sha S, Hong MS, Maloney AJ, Barone PW, Neufeld C, Wolfrum J, Springs SL, Sinskey AJ, Braatz RD. Mechanistic model for production of recombinant adeno-associated virus via triple transfection of HEK293 cells. Mol Ther Methods Clin Dev 2021; 21:642-655. [PMID: 34095346 PMCID: PMC8143981 DOI: 10.1016/j.omtm.2021.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/08/2021] [Indexed: 02/08/2023]
Abstract
Manufacturing of recombinant adeno-associated virus (rAAV) viral vectors remains challenging, with low yields and low full:empty capsid ratios in the harvest. To elucidate the dynamics of recombinant viral production, we develop a mechanistic model for the synthesis of rAAV viral vectors by triple plasmid transfection based on the underlying biological processes derived from wild-type AAV. The model covers major steps starting from exogenous DNA delivery to the reaction cascade that forms viral proteins and DNA, which subsequently result in filled capsids, and the complex functions of the Rep protein as a regulator of the packaging plasmid gene expression and a catalyst for viral DNA packaging. We estimate kinetic parameters using dynamic data from literature and in-house triple transient transfection experiments. Model predictions of productivity changes as a result of the varied input plasmid ratio are benchmarked against transfection data from the literature. Sensitivity analysis suggests that (1) the poorly coordinated timeline of capsid synthesis and viral DNA replication results in a low ratio of full virions in harvest, and (2) repressive function of the Rep protein could be impeding capsid production at a later phase. The analyses from the mathematical model provide testable hypotheses for evaluation and reveal potential process bottlenecks that can be investigated.
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Affiliation(s)
- Tam N.T. Nguyen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sha Sha
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Moo Sun Hong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew J. Maloney
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul W. Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caleb Neufeld
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacqueline Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stacy L. Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anthony J. Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Richard D. Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
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11
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Su J, Rice J, Hoffman J, Alvarado S, Bailey M, Kopp M, Murphy M, Kiss R, Barone PW, Wiebe ME, Springs SL, Dehghani H, Chen D. Revisiting mouse minute virus inactivation by high temperature short time treatment. Biotechnol Bioeng 2021; 118:2967-2976. [PMID: 33913515 DOI: 10.1002/bit.27805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022]
Abstract
In recent years, high temperature short time (HTST) treatment technology has been increasingly adopted for medium treatment to mitigate the potential risk of viral contamination in mammalian cell culture GMP manufacturing facilities. Mouse minute virus (MMV), also called minute virus of mice (MVM), implicated in multiple viral contamination events is commonly used as a relevant model virus to assess the effectiveness of HTST treatment of cell culture media. However, results from different studies vary broadly in inactivation kinetics as well as log reduction factors (LRFs) achieved under given treatment conditions. To determine whether the reported discrepancies stemmed from differences in MMV strains, laboratory-scale HTST devices, medium matrices, and/or experimental designs, we have taken a collaborative approach to systematically assess the effectiveness of HTST treatment for MMV inactivation. This effort was conceptualized based on a media treatment gap analysis conducted by the Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) under the MIT Center for Biomedical Innovation (CBI). Specifically, two different MMV strains were used to evaluate the effectiveness of HTST at various treatment conditions with regard to exposure temperature and hold time duration by two independent laboratories within two different companies. To minimize experimental variations, the two sites used the same batches of MMV stocks, the same commercially purchased medium, and the same model of thermocyclers as the laboratory-scale HTST device. The two independent laboratories yielded similar MMV inactivation kinetics and comparable LRF. No significant differences were observed between the two MMV strains evaluated, suggesting that the variations from prior studies were likely due to differences in equipment, medium matrices, or other factors. The data presented here indicate that MMV inactivation by HTST treatment obeys first-order kinetics and can be mathematically modeled using an Arrhenius equation. The model-based extrapolation provides a quantitative estimate of MMV inactivation by the current industry standard HTST condition (102°C for a hold time of 10 s) used for medium treatment. Finally, based on the data from the current study and the industry experience, it is recommended that any alternative virus barrier technologies adopted for medium treatment should provide a clearance of at least 3.0 LRF based on a worst-case model virus to effectively mitigate potential risks of viral contamination.
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Affiliation(s)
- Joleen Su
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - Jonathan Rice
- Biosafety Development Laboratory, Amgen Inc., Thousand Oaks, California, USA
| | - Jacob Hoffman
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - Shelley Alvarado
- Biosafety Development Laboratory, Amgen Inc., Thousand Oaks, California, USA
| | - Mark Bailey
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - Martina Kopp
- Biosafety Development Laboratory, Amgen Inc., Thousand Oaks, California, USA
| | - Marie Murphy
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - Robert Kiss
- Process and Analytical Development, Sutro Biopharma, South San Francisco, California, USA
| | - Paul W Barone
- Center for Biomedical Innovation, MIT, Cambridge, Massachusetts, USA
| | - Michael E Wiebe
- Center for Biomedical Innovation, MIT, Cambridge, Massachusetts, USA
| | - Stacy L Springs
- Center for Biomedical Innovation, MIT, Cambridge, Massachusetts, USA
| | - Houman Dehghani
- Operations Technology, Allogene Therapeutics, South San Francisco, California, USA
| | - Dayue Chen
- Bioproduct Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA.,Pharma Technical Development, Genentech, a Member of the Roche Group, 1 DNA Way, South San Francisco, California, USA
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12
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Wu X, Tay JK, Goh CK, Chan C, Lee YH, Springs SL, Wang DY, Loh KS, Lu TK, Yu H. Digital CRISPR-based method for the rapid detection and absolute quantification of nucleic acids. Biomaterials 2021; 274:120876. [PMID: 34034027 DOI: 10.1016/j.biomaterials.2021.120876] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/23/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022]
Abstract
Rapid diagnostics of adventitious agents in biopharmaceutical/cell manufacturing release testing and the fight against viral infection have become critical. Quantitative real-time PCR and CRISPR-based methods rapidly detect DNA/RNA in 1 h but suffer from inter-site variability. Absolute quantification of DNA/RNA by methods such as digital PCR reduce this variability but are currently too slow for wider application. Here, we report a RApid DIgital Crispr Approach (RADICA) for absolute quantification of nucleic acids in 40-60 min. Using SARS-CoV-2 as a proof-of-concept target, RADICA allows for absolute quantification with a linear dynamic range of 0.6-2027 copies/μL (R2 value > 0.99), high accuracy and low variability, no cross-reactivity to similar targets, and high tolerance to human background DNA. RADICA's versatility is validated against other targets such as Epstein-Barr virus (EBV) from human B cells and patients' serum. RADICA can accurately detect and absolutely quantify EBV DNA with similar dynamic range of 0.5-2100 copies/μL (R2 value > 0.98) in 1 h without thermal cycling, providing a 4-fold faster alternative to digital PCR-based detection. RADICA therefore enables rapid and sensitive absolute quantification of nucleic acids which can be widely applied across clinical, research, and biomanufacturing areas.
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Affiliation(s)
- Xiaolin Wu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Joshua K Tay
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Chuan Keng Goh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Cheryl Chan
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Yie Hou Lee
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Stacy L Springs
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - De Yun Wang
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Kwok Seng Loh
- Department of Otolaryngology-Head and Neck Surgery, National University of Singapore, Singapore
| | - Timothy K Lu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02142, USA.
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore; Institute of Bioengineering and Bioimaging, A*STAR, The Nanos, #04-01, 31, Biopolis Way, 138669, Singapore; Mechanobiology Institute, National University of Singapore, T-Lab, #05-01, 5A Engineering Drive 1, 117411, Singapore; Department of Physiology & the Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, MD9-04-11, 2 Medical Drive, 117593, Singapore.
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13
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Guttieres D, Sinskey AJ, Springs SL. Models to inform neutralizing antibody therapy strategies during pandemics: the case of SARS-CoV-2. Antib Ther 2021; 4:60-71. [PMID: 33928236 PMCID: PMC8022923 DOI: 10.1093/abt/tbab006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/09/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
Background Neutralizing antibodies (nAbs) against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) can play an important role in reducing impacts of the COVID-19 pandemic, complementing ongoing public health efforts such as diagnostics and vaccination. Rapidly designing, manufacturing and distributing nAbs requires significant planning across the product value chain and an understanding of the opportunities, challenges and risks throughout. Methods A systems framework comprised of four critical components is presented to aid in developing effective end-to-end nAbs strategies in the context of a pandemic: (1) product design and optimization, (2) epidemiology, (3) demand and (4) supply. Quantitative models are used to estimate product demand using available epidemiological data, simulate biomanufacturing operations from typical bioprocess parameters and calculate antibody production costs to meet clinical needs under various realistic scenarios. Results In a US-based case study during the 9-month period from March 15 to December 15, 2020, the projected number of SARS-CoV-2 infections was 15.73 million. The estimated product volume needed to meet therapeutic demand for the maximum number of clinically eligible patients ranged between 6.3 and 31.5 tons for 0.5 and 2.5 g dose sizes, respectively. The relative production scale and cost needed to meet demand are calculated for different centralized and distributed manufacturing scenarios. Conclusions Meeting demand for anti-SARS-CoV-2 nAbs requires significant manufacturing capacity and planning for appropriate administration in clinical settings. MIT Center for Biomedical Innovation’s data-driven tools presented can help inform time-critical decisions by providing insight into important operational and policy considerations for making nAbs broadly accessible, while considering time and resource constraints.
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Affiliation(s)
- Donovan Guttieres
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anthony J Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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14
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Gimpel AL, Katsikis G, Sha S, Maloney AJ, Hong MS, Nguyen TNT, Wolfrum J, Springs SL, Sinskey AJ, Manalis SR, Barone PW, Braatz RD. Analytical methods for process and product characterization of recombinant adeno-associated virus-based gene therapies. Mol Ther Methods Clin Dev 2021; 20:740-754. [PMID: 33738328 PMCID: PMC7940698 DOI: 10.1016/j.omtm.2021.02.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The optimization of upstream and downstream processes for production of recombinant adeno-associated virus (rAAV) with consistent quality depends on the ability to rapidly characterize critical quality attributes (CQAs). In the context of rAAV production, the virus titer, capsid content, and aggregation are identified as potential CQAs, affecting the potency, purity, and safety of rAAV-mediated gene therapy products. Analytical methods to measure these attributes commonly suffer from long turnaround times or low throughput for process development, although rapid, high-throughput methods are beginning to be developed and commercialized. These methods are not yet well established in academic or industrial practice, and supportive data are scarce. Here, we review both established and upcoming analytical methods for the quantification of rAAV quality attributes. In assessing each method, we highlight the progress toward rapid, at-line characterization of rAAV. Furthermore, we identify that a key challenge for transitioning from traditional to newer methods is the scarcity of academic and industrial experience with the latter. This literature review serves as a guide for the selection of analytical methods targeting quality attributes for rapid, high-throughput process characterization during process development of rAAV-mediated gene therapies.
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Affiliation(s)
- Andreas L Gimpel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Georgios Katsikis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sha Sha
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew John Maloney
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Moo Sun Hong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tam N T Nguyen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jacqueline Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
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15
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Barone PW, Wiebe ME, Leung JC, Hussein ITM, Keumurian FJ, Bouressa J, Brussel A, Chen D, Chong M, Dehghani H, Gerentes L, Gilbert J, Gold D, Kiss R, Kreil TR, Labatut R, Li Y, Müllberg J, Mallet L, Menzel C, Moody M, Monpoeho S, Murphy M, Plavsic M, Roth NJ, Roush D, Ruffing M, Schicho R, Snyder R, Stark D, Zhang C, Wolfrum J, Sinskey AJ, Springs SL. Viral contamination in biologic manufacture and implications for emerging therapies. Nat Biotechnol 2020; 38:563-572. [DOI: 10.1038/s41587-020-0507-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 04/01/2020] [Indexed: 01/02/2023]
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16
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Abstract
Cybersecurity for the production of safe and effective biopharmaceuticals requires the attention of multiple stakeholders, including industry, governments, and healthcare providers. Cyberbiosecurity breaches could directly impact patients, from compromised data privacy to disruptions in production that jeopardize global pandemic response. Maintaining cybersecurity in the modern economy, where advanced manufacturing technologies and digital strategies are becoming the norm, is a significant challenge. Here, we highlight vulnerabilities in present and future biomanufacturing paradigms given the dependence of this industry sector on proprietary intellectual property, cyber-physical systems, and government-regulated production environments, as well as movement toward advanced manufacturing models. Specifically, we (1) present an analysis of digital information flow in a typical biopharmaceutical manufacturing value chain; (2) consider the potential cyberbiosecurity risks that might emerge from advanced manufacturing models such as continuous and distributed systems; and (3) provide recommendations for risk mitigation. While advanced manufacturing models hold the potential for reducing costs and increasing access to more personalized therapies, the evolving landscape of the biopharmaceutical enterprise has led to growing concerns over potential cyber attacks. Gaining better foresight on potential risks is key for implementing proactive defensive principles, framing new developments, and establishing a permanent security culture that adapts to new challenges while maintaining the transparency required for regulated production of safe and effective medicines.
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Affiliation(s)
- Donovan Guttieres
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Shannon Stewart
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Jacqueline Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, United States
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17
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Barone PW, Avgerinos S, Ballard R, Brussel A, Clark P, Dowd C, Gerentes L, Hart I, Keumurian FJ, Kindermann J, Leung JC, Ly N, Mink S, Minning S, Mullberg J, Murphy M, Nöske K, Parriott S, Shum B, Wiebe ME, Springs SL. Biopharmaceutical Industry Approaches to Facility Segregation for Viral Safety: An Effort from the Consortium on Adventitious Agent Contamination in Biomanufacturing. PDA J Pharm Sci Technol 2018; 73:191-203. [PMID: 30361281 DOI: 10.5731/pdajpst.2018.008862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Appropriate segregation within manufacturing facilities is required by regulators and utilized by manufacturers to ensure that the final product has not been contaminated with (a) adventitious viruses, (b) another pre-/postviral clearance fraction of the same product, or (c) another product processed in the same facility. However, there is no consensus on what constitutes appropriate facility segregation to minimize these risks. In part, this is due to the fact that a wide variety of manufacturing facilities and operational practices exist, including single-product and multiproduct manufacturing, using traditional segregation strategies with separate rooms for specific operations that may use stainless steel or disposable equipment to more modern ballroom-style operations that use mostly disposable equipment (i.e., pre- and postviral clearance manufacturing operations are not physically segregated by walls). Further, consensus is lacking around basic definitions and approaches related to facility segregation. For example, given that several unit operations provide assurance of virus clearance during downstream processing, how does one define pre- and postviral clearance and at which point(s) should a viral segregation barrier be introduced? What is a "functionally closed" system? How can interventions be conducted so that the system remains functionally closed? How can functionally closed systems be used to adequately isolate a product stream and ensure its safety? To address these issues, the member companies of the Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) have conducted a facility segregation project with the following goals: define "pre- and postviral clearance zones" and "pre- and postviral clearance materials"; define "functionally closed" manufacturing systems; and identify an array of facility segregation approaches that are used for the safe and effective production of recombinant biologics as well as plasma products. This article reflects the current thinking from this collaborative endeavor.LAY ABSTRACT: Operations in biopharmaceutical manufacturing are segregated to ensure that the final product has not been contaminated with adventitious viruses, another fraction of the same product, or with another product from within the same facility. Yet there is no consensus understanding of what appropriate facility segregation looks like. There are a wide variety of manufacturing facilities and operational practices. There are existing facilities with separate rooms and more modern approaches that use disposable equipment in an open ballroom without walls. There is also no agreement on basic definitions and approaches related to facility segregation approaches. For example, many would like to claim that their manufacturing process is functionally closed, yet exactly how a functionally closed system may be defined is not clear. To address this, the member companies of the Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) have conducted a project with the goal of defining important manufacturing terms relevant to designing an appropriately segregated facility and identifying different facility segregation approaches that are used for the safe and effective production of recombinant biologics as well as plasma products.
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Affiliation(s)
- Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA;
| | | | | | | | | | | | | | - Ian Hart
- MedImmune, Gaithersburg, MD, USA
| | - Flora J Keumurian
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - James C Leung
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nguyen Ly
- Merck & Co., Inc., Kenilworth, NJ, USA
| | | | | | | | | | | | | | | | - Michael E Wiebe
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
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18
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Stewart SR, Barone PW, Bellisario A, Cooney CL, Sharp PA, Sinskey AJ, Natesan S, Springs SL. Leveraging Industry-Academia Collaborations in Adaptive Biomedical Innovation. Clin Pharmacol Ther 2016; 100:647-653. [PMID: 27617845 DOI: 10.1002/cpt.504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/25/2016] [Indexed: 11/05/2022]
Abstract
Despite the rapid pace of biomedical innovation, research and development (R&D) productivity in the pharmaceutical industry has not improved broadly. Increasingly, firms need to leverage new approaches to product development and commercial execution, while maintaining adaptability to rapid changes in the marketplace and in biomedical science. Firms are also seeking ways to capture some of the talent, infrastructure, and innovation that depends on federal R&D investment. As a result, a major transition to external innovation is taking place across the industry. One example of these external innovation initiatives is the Sanofi-MIT Partnership, which provided seed funding to MIT investigators to develop novel solutions and approaches in areas of interest to Sanofi. These projects were highly collaborative, with information and materials flowing both ways. The relatively small amount of funding and short time frame of the awards built an adaptable and flexible process to advance translational science.
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Affiliation(s)
- S R Stewart
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - P W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - A Bellisario
- Technology Licensing Office, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - C L Cooney
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - P A Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - A J Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - S Natesan
- Sanofi, Cambridge, Massachusetts, USA
| | - S L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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19
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Abstract
Measurements of peroxidase activities of two site-specific mutants and wild type cytochrome b562 suggest that the enzymatic activity correlates with the redox potential of the metal center. A lower value of the Fe(3+)/Fe(2+) redox potential seems to be important for promoting peroxidase activity of the hemeprotein possibly by stabilization of the high-valent redox intermediate involved in the catalytic function. The results provide an approach towards rational tuning of enzyme function when 'grafted' into a new protein environment.
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20
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Springs SL, Diavolitsis VM, Goodhouse J, McLendon GL. The kinetics of translocation of Smac/DIABLO from the mitochondria to the cytosol in HeLa cells. J Biol Chem 2002; 277:45715-8. [PMID: 12364342 DOI: 10.1074/jbc.c200524200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Smac (second mitochondrial activator of caspases) is released from the mitochondria during apoptosis to relieve inhibition of caspases by the inhibitor of apoptosis proteins (IAPs). The release of Smac antagonizes several IAPs and assists the initiator caspase-9 and effector caspases (caspase-3, caspase-6, and caspase-7) in becoming active, ultimately leading to death of the cell. Translocation of Smac along with cytochrome c and other mitochondrial pro-apoptotic proteins represent important regulatory checkpoints for mitochondria-mediated apoptosis. Whether Smac and cytochrome c translocate by the same mechanism is not known. Here, we show that the time required for Smac efflux from the mitochondria of cells subjected to staurosporine-induced apoptosis is approximately four times longer than the time required for cytochrome c efflux. These results suggest that Smac and cytochrome c may exit the mitochondria by different pathways.
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Affiliation(s)
- Stacy L Springs
- Department of Chemistry and the Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.
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21
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22
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Springs SL, Bass SE, Bowman G, Nodelman I, Schutt CE, McLendon GL. A multigeneration analysis of cytochrome b(562) redox variants: evolutionary strategies for modulating redox potential revealed using a library approach. Biochemistry 2002; 41:4321-8. [PMID: 11914078 DOI: 10.1021/bi012066s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The redox potential of cytochromes sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed. Here, the heme protein, cytochrome b(562), is used to study the in vitro evolution of redox potential within a library of variants containing the same structural archetype, the four-helix bundle. Multisite variations in the active site of cytochrome b(562) were introduced. A library of variants containing random mutations in place of R98 and R106 was created, and the redox potentials of a statistical sampling of this library were measured. This procedure was carried out for both the low- and high-potential variants of a previously studied F61X/F65X, first-generation library [Springs, S. L., Bass, S. E., and McLendon, G. L. (2000) Biochemistry 39, 6075]. The second-generation library reported here has a range of redox potentials which is greater than 40% (160 mV) of the known accessible potential among cytochromes with identical axial ligands (but different folds) and exceeds the range exhibited phylogenetically by the cytochrome c' family which internally maintains the same axial ligation and fold. A statistical analysis of the libraries examined reveals that the redox potential of WT cyt b(562) is found at the high-potential extremum of the distribution, indicating that this protein apparently evolved to differentially stabilize the reduced protein. The 2.7 A crystal structure of F61I/F65Y/R106L (low-potential variant of the second-generation library) was solved and is compared to the wild-type structure and the 2.2 A resolution structure of the F61I/F65Y variant (low-potential variant of the first-generation library). The structures indicate that charge-dipole effects are responsible for shifting the redox equilibrium toward the oxidized state in both the F61I/F65Y and F61I/F65Y/R106L variants. Specifically, a new protein dipole is introduced into the heme microenvironment as a result of the F65Y mutation, two new internal water molecules (one in hydrogen-bonding distance of Y65) are found, and in the case of F61I/F65Y/R106L (DeltaE(m) = 158 mV vs NHE), increased solvent exposure of the heme as a result of the R106L substitution is identified.
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Affiliation(s)
- Stacy L Springs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.
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23
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Abstract
A general understanding of how cytochromes evolve within a fixed structure to optimize redox potential for specific bioenergetic processes does not exist. Toward this end, a library approach is used to investigate the range and distribution of redox potential which occurs when all sequence space available through mutation at two positions is examined within a fixed structural motif. Random mutation of Phe61 and Phe65 of cytochrome b562 (E. coli), and subsequent examination of a statistically significant sampling of this library, demonstrates that the redox potential can vary over 100 mV (>25% of the known accessible potential in native proteins with axial His-Met ligation) through mutation at these two positions. The redox potential of the wild-type protein occurs at an extremum of the distribution observed, indicating that Phe61 and Phe65 were most likely naturally selected to differentially stabilize the reduced state of the protein. At the other extremum, a compositionally conservative set of mutations (F61I, F65Y) leads to a 100 mV shift in the redox equilibrium toward the oxidized state. NMR analyses indicate that a charge-dipole interaction which results from mutation of phenylalanine to tyrosine at position 65 may be responsible.
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Affiliation(s)
- S L Springs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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24
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Springs SL, Gosztola D, Wasielewski MR, Král V, Andrievsky A, Sessler JL. Picosecond Dynamics of Energy Transfer in Porphyrin−Sapphyrin Noncovalent Assemblies. J Am Chem Soc 1999. [DOI: 10.1021/ja9835436] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stacy L. Springs
- Contribution from the Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, Argonne National Laboratory, Chicago, Illinois, and the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - David Gosztola
- Contribution from the Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, Argonne National Laboratory, Chicago, Illinois, and the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Michael R. Wasielewski
- Contribution from the Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, Argonne National Laboratory, Chicago, Illinois, and the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Vladimír Král
- Contribution from the Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, Argonne National Laboratory, Chicago, Illinois, and the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Andrei Andrievsky
- Contribution from the Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, Argonne National Laboratory, Chicago, Illinois, and the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Jonathan L. Sessler
- Contribution from the Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, Argonne National Laboratory, Chicago, Illinois, and the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
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Sessler JL, Brown CT, O'Connor D, Springs SL, Wang R, Sathiosatham M, Hirose T. A Rigid Chlorin-Naphthalene Diimide Conjugate. A Possible New Noncovalent Electron Transfer Model System. J Org Chem 1998; 63:7370-7374. [PMID: 11672385 DOI: 10.1021/jo9810112] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Described in this paper is the synthesis and study of a rigid "coplanar" noncovalent electron-transfer model system. This putative noncovalent complex juxtaposes a novel donor (chlorin) and acceptor (naphthalene diimide) via a three-point hydrogen bonding interaction (CDCl(3), K(a) = 364 +/- 47 M(-)(1)). It was studied by steady state fluorescence, time-resolved luminescence, and transient absorption methods. The results of the studies are consistent with (1) forward intraensemble electron transfer (ET) taking place rapidly following photoexcitation of the chlorin donor at 575 nm (k(ET) = 7.6 x 10(8) s(-)(1); DeltaG(cs) approximately -457 mV; Phi = 0.91) and (2) back electron transfer occurring even more rapidly.
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Affiliation(s)
- Jonathan L. Sessler
- Department of Chemistry and Biochemistry, University of Texas at Austin, Texas 78712
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Arimura T, Brown CT, Springs SL, Sessler JL. Intracomplex electron transfer in a hydrogen-bonded calixarene–porphyrin system. Chem Commun (Camb) 1996. [DOI: 10.1039/cc9960002293] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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