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2. Engineered SARS-CoV-2 receptor binding domain improves manufacturability in yeast and immunogenicity in mice

Author

Dalvie, Neil C., Rodriguez-Aponte, Sergio A., Hartwell, Brittany L., Tostanoski, Lisa H., Biedermann, Andrew M., Crowell, Laura E., Kaur, Kawaljit, Kumru, Ozan S., Carter, Lauren, Yu, Jingyou, Chang, Aiquan, McMahan, Katherine, Courant, Thomas, Lebas, Celia, Lemnios, Ashley A., Rodrigues, Kristen A., Silva, Murillo, Johnston, Ryan S., Naranjo, Christopher A., Tracey, Mary Kate, Brady, Joseph R., Whittaker, Charles A., Yun, Dongsoo, Brunette, Natalie, Wang, Jing Yang, Walkey, Carl, Fiala, Brooke, Kar, Swagata, Porto, Maciel, Lok, Megan, Andersen, Hanne, Lewis, Mark G., Love, Kerry R., Camp, Danielle L., Silverman, Judith Maxwell, Kleanthous, Harry, Joshi, Sangeeta B., Volkin, David B., Dubois, Patrice M., Collin, Nicolas, King, Neil P., Barouch, Dan H., Irvine, Darrell J., and Love, J. Christopher

Published
2021

3. Rapid Developability Assessments to Formulate Recombinant Protein Antigens as Stable, Low-Cost, Multi-Dose Vaccine Candidates: Case-Study With Non-Replicating Rotavirus (NRRV) Vaccine Antigens

Author

Sawant, Nishant, Kaur, Kawaljit, Holland, David A., Hickey, John M., Agarwal, Sanjeev, Brady, Joseph R., Dalvie, Neil C., Tracey, Mary Kate, Velez-Suberbie, M. Lourdes, Morris, Stephen A., Jacob, Shaleem I., Bracewell, Daniel G., Mukhopadhyay, Tarit K., Love, Kerry R., Love, J. Christopher, Joshi, Sangeeta B., and Volkin, David B.

Published
2021
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5. Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus

Author

Dalvie, Neil C., Brady, Joseph R., Crowell, Laura E., Tracey, Mary Kate, Biedermann, Andrew M., Kaur, Kawaljit, Hickey, John M., Kristensen, II, D. Lee, Bonnyman, Alexandra D., Rodriguez-Aponte, Sergio A., Whittaker, Charles A., Bok, Marina, Vega, Celina, Mukhopadhyay, Tarit K., Joshi, Sangeeta B., Volkin, David B., Parreño, Viviana, Love, Kerry R., and Love, J. Christopher

Published
2021
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11. Additional file 1 of Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus

Author

Dalvie, Neil C., Brady, Joseph R., Crowell, Laura E., Tracey, Mary Kate, Biedermann, Andrew M., Kaur, Kawaljit, Hickey, John M., Kristensen, D. Lee, Bonnyman, Alexandra D., Rodriguez-Aponte, Sergio A., Whittaker, Charles A., Bok, Marina, Vega, Celina, Mukhopadhyay, Tarit K., Joshi, Sangeeta B., Volkin, David B., Parreño, Viviana, Love, Kerry R., and Love, J. Christopher

Subjects
Data_FILES
Abstract

Additional file 1. Additional Tables and Figures.

Published
2021
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13. Development of a platform process for the production and purification of single‐domain antibodies

Author

Crowell, Laura E., primary, Goodwine, Chaz, additional, Holt, Carla S., additional, Rocha, Lucia, additional, Vega, Celina, additional, Rodriguez, Sergio A., additional, Dalvie, Neil C., additional, Tracey, Mary K., additional, Puntel, Mariana, additional, Wigdorovitz, Andrés, additional, Parreño, Viviana, additional, Love, Kerry R., additional, Cramer, Steven M., additional, and Love, J. Christopher, additional

Published
2021
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14. Engineered SARS-CoV-2 receptor binding domain improves immunogenicity in mice and elicits protective immunity in hamsters

Author

Dalvie, Neil C., primary, Rodriguez-Aponte, Sergio A., additional, Hartwell, Brittany L., additional, Tostanoski, Lisa H., additional, Biedermann, Andrew M., additional, Crowell, Laura E., additional, Kaur, Kawaljit, additional, Kumru, Ozan, additional, Carter, Lauren, additional, Yu, Jingyou, additional, Chang, Aiquan, additional, McMahan, Katherine, additional, Courant, Thomas, additional, Lebas, Celia, additional, Lemnios, Ashley A., additional, Rodrigues, Kristen A., additional, Silva, Murillo, additional, Johnston, Ryan S., additional, Naranjo, Christopher A., additional, Tracey, Mary Kate, additional, Brady, Joseph R., additional, Whittaker, Charles A., additional, Yun, Dongsoo, additional, Kar, Swagata, additional, Porto, Maciel, additional, Lok, Megan, additional, Andersen, Hanne, additional, Lewis, Mark G., additional, Love, Kerry R., additional, Camp, Danielle L., additional, Silverman, Judith Maxwell, additional, Kleanthous, Harry, additional, Joshi, Sangeeta B., additional, Volkin, David B., additional, Dubois, Patrice M., additional, Collin, Nicolas, additional, King, Neil P., additional, Barouch, Dan H., additional, Irvine, Darrell J., additional, and Love, J. Christopher, additional

Published
2021
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17. Molecular Engineering Improves Antigen Quality and Enables Integrated Manufacturing of A Trivalent Subunit Vaccine Candidate for Rotavirus

Author

Dalvie, Neil, primary, Brady, Joseph, additional, Crowell, Laura, additional, Tracey, Mary Kate, additional, Biedermann, Andrew, additional, Kaur, Kawalijt, additional, Hickey, John M., additional, Kristensen, Duane Lee, additional, Bonnyman, Alexandra, additional, Rodriguez-Aponte, Sergio, additional, Whittaker, Charles, additional, Bok, Marina, additional, Vega, Celina, additional, Mukhopadhyay, Tarit, additional, Joshi, Sangeeta, additional, Volkin, David, additional, Parreno, Viviana, additional, Love, Kerry R., additional, and Love, J. Christopher, additional

Published
2020
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18. Molecular engineering improves antigen quality and enables integrated manufacturing of a trivalent subunit vaccine candidate for rotavirus

Author

Dalvie, Neil C., primary, Brady, Joseph R., additional, Crowell, Laura E., additional, Tracey, Mary Kate, additional, Biedermann, Andrew M., additional, Kaur, Kawaljit, additional, Hickey, John M., additional, Kristensen, D. Lee, additional, Bonnyman, Alexandra, additional, Rodriguez-Aponte, Sergio A., additional, Whittaker, Charles A., additional, Bok, Marina, additional, Vega, Celina, additional, Mukhopadhyay, Tarit, additional, Joshi, Sangeeta B., additional, Volkin, David B., additional, Parreño, Viviana, additional, Love, Kerry R., additional, and Love, J. Christopher, additional

Published
2020
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20. Modular development enables rapid design of media for alternative hosts.

Author

Biedermann, Andrew M., Gengaro, Isabella R., Rodriguez‐Aponte, Sergio A., Love, Kerry R., and Love, J. Christopher

Abstract

Developing media to sustain cell growth and production is an essential and ongoing activity in bioprocess development. Modifications to media can often address host or product‐specific challenges, such as low productivity or poor product quality. For other applications, systematic design of new media can facilitate the adoption of new industrially relevant alternative hosts. Despite manifold existing methods, common approaches for optimization often remain time and labor‐intensive. We present here a novel approach to conventional media blending that leverages stable, simple, concentrated stock solutions to enable rapid improvement of measurable phenotypes of interest. We applied this modular methodology to generate high‐performing media for two phenotypes of interest: biomass accumulation and heterologous protein production, using high‐throughput, milliliter‐scale batch fermentations of Pichia pastoris as a model system. In addition to these examples, we also created a flexible open‐source package for modular blending automation on a low‐cost liquid handling system to facilitate wide use of this method. Our modular blending method enables rapid, flexible media development, requiring minimal labor investment and prior knowledge of the host organism, and should enable developing improved media for other hosts and phenotypes of interest. [ABSTRACT FROM AUTHOR]

Published
2022
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22. Macroscopic modeling of bioreactors for recombinant protein producing Pichia pastoris in defined medium.

Author

Hong, Moo Sun, Velez‐Suberbie, M. Lourdes, Maloney, Andrew J., Biedermann, Andrew, Love, Kerry R., Love, J. Christopher, Mukhopadhyay, Tarit K., and Braatz, Richard D.

Abstract

The methylotrophic yeast Pichia pastoris is widely used as a microbial host for recombinant protein production. Bioreactor models for P. pastoris can inform understanding of cellular metabolism and can be used to optimize bioreactor operation. This article constructs an extensive macroscopic bioreactor model for P. pastoris which describes substrates, biomass, total protein, other medium components, and off‐gas components. Species and elemental balances are introduced to describe uptake and evolution rates for medium components and off‐gas components. Additionally, a pH model is constructed using an overall charge balance, acid/base equilibria, and activity coefficients to describe production of recombinant protein and precipitation of medium components. The extent of run‐to‐run variability is modeled by distributions of a subset of the model parameters, which are estimated using the maximum likelihood method. Model prediction from the extensive macroscopic bioreactor model well describes experimental data with different operating conditions. The probability distributions of the model predictions quantified from the parameter distribution are quantifiably consistent with the run‐to‐run variability observed in the experimental data. The uncertainty description in this macroscopic bioreactor model identifies the model parameters that have large variability and provides guidance as to which aspects of cellular metabolism should be the focus of additional experimental studies. The model for medium components with pH and precipitation can be used for improving chemically defined medium by minimizing the amount of components needed while meeting cellular requirements. [ABSTRACT FROM AUTHOR]

Published
2021
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24. On-demand manufacturing of clinical-quality biopharmaceuticals

Author

Crowell, Laura E, primary, Lu, Amos E, additional, Love, Kerry R, additional, Stockdale, Alan, additional, Timmick, Steven M, additional, Wu, Di, additional, Wang, Yu (Annie), additional, Doherty, William, additional, Bonnyman, Alexandra, additional, Vecchiarello, Nicholas, additional, Goodwine, Chaz, additional, Bradbury, Lisa, additional, Brady, Joseph R, additional, Clark, John J, additional, Colant, Noelle A, additional, Cvetkovic, Aleksandar, additional, Dalvie, Neil C, additional, Liu, Diana, additional, Liu, Yanjun, additional, Mascarenhas, Craig A, additional, Matthews, Catherine B, additional, Mozdzierz, Nicholas J, additional, Shah, Kartik A, additional, Wu, Shiaw-Lin, additional, Hancock, William S, additional, Braatz, Richard D, additional, Cramer, Steven M, additional, and Love, J Christopher, additional

Published
2018
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27. Characterization of Site-Specific Glycosylation in Influenza A Virus Hemagglutinin Produced by Spodoptera frugiperdaInsect Cell Line

Author

Liu, Yan-Jun, Wu, Shiaw-Lin, Love, Kerry R., and Hancock, William S.

Abstract

Influenza hemagglutinin is a surface glycoprotein related to virus invasion and host immune system response. Understanding site specific glycosylation of hemagglutinin will increase our knowledge about virus evolution and can improve the design and quality of vaccines. In our study, we used glycoproteomic analysis based on multienzyme digestion followed by LC tandem MS analysis to determine the glycosylation of Influenza hemagglutinin (H1/A/California/04/2009) using the following steps: PNGaseF treatment combined with trypsin or pepsin digestion was used to determine the glycosites and glycan occupancy. Three enzymes, trypsin, AspN, and pepsin, were used separately to generate suitable glycopeptides for online LC tandem MS analysis. The glycan structure of a given glycopeptide was determined by collision-induced dissociation MS/MS fragmentation, and the peptide backbone information was provided by collision-induced dissociation (CID)-MS3 fragmentation. With this approach, 100% sequence coverage of the hemagglutinin sample was obtained. Six glycosylation sites fitting the sequon N-X-S/T were successfully confirmed, and the glycan heterogeneity as well as the ratios of glycoforms were determined at each site.

Published
2024
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31. Integrated Bottom-Up and Top-Down Liquid Chromatography–Mass Spectrometry for Characterization of Recombinant Human Growth Hormone Degradation Products

Author

Wang, Yu Annie, primary, Wu, Di, additional, Auclair, Jared R., additional, Salisbury, Joseph P., additional, Sarin, Richa, additional, Tang, Yang, additional, Mozdzierz, Nicholas J., additional, Shah, Kartik, additional, Zhang, Anna Fan, additional, Wu, Shiaw-lin, additional, Agar, Jeffery N., additional, Love, J. Christopher, additional, Love, Kerry R., additional, and Hancock, William S., additional

Published
2017
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34. Erratum to: Comparative genomics and transcriptomics of Pichia pastoris

Author

Love, Kerry R., primary, Shah, Kartik A., additional, Whittaker, Charles A., additional, Wu, Jie, additional, Bartlett, M. Catherine, additional, Ma, Duanduan, additional, Leeson, Rachel L., additional, Priest, Margaret, additional, Borowsky, Jonathan, additional, Young, Sarah K., additional, and Love, J. Christopher, additional

Published
2016
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35. Comparative genomics and transcriptomics of Pichia pastoris

Author

Love, Kerry R., primary, Shah, Kartik A., additional, Whittaker, Charles A., additional, Wu, Jie, additional, Bartlett, M. Catherine, additional, Ma, Duanduan, additional, Leeson, Rachel L., additional, Priest, Margaret, additional, Borowsky, Jonathan, additional, Young, Sarah K., additional, and Love, J. Christopher, additional

Published
2016
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37. Development of a general defined medium for Pichia pastoris.

Author

Matthews, Catherine B., Kuo, Angel, Love, Kerry R., and Love, J. Christopher

Abstract

Pichia pastoris is widely used as a host for recombinant protein production. More than 500 proteins have been expressed in the organism at a variety of cultivation scales, from small shake flasks to large bioreactors. Large-scale fermentation strategies typically employ chemically defined growth medium because of its greater batch-to-batch consistency and in many cases, lower costs compared to complex medium. For biopharmaceuticals, defined growth medium may also simplify downstream purification and regulatory documentation. Standard formulations of defined media for P. pastoris are minimal ones that lack the metabolic intermediates provided by complex components such as peptone and yeast extract. As a result, growth rates and per-cell productivities are significantly lower than in complex medium. We have designed a rich defined medium (RDM) for Pichia pastoris by systematically evaluating nutrients of increasing complexity and identifying those that are most critical for growth. We have also employed transcriptomics to gain deeper insights into the underlying metabolic processes and inform our media design. We have demonstrated that using RDM for expression of three heterologous proteins yields titers comparable to, or higher than, those in standard complex medium. RDM improves productivity of P. pastoris fermentations and its development demonstrates the usefulness of transcriptomics to accelerate process development for new molecules. [ABSTRACT FROM AUTHOR]

Published
2018
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47. Erratum to: Comparative genomics and transcriptomics of Pichia pastoris

Author

J. Christopher Love, Kartik A. Shah, Charles A. Whittaker, Jie Wu, Kerry R. Love, Margaret Priest, Jonathan Borowsky, Rachel Leeson, Sarah Young, Duanduan Ma, M. Catherine Bartlett, Massachusetts Institute of Technology. Department of Chemical Engineering, Koch Institute for Integrative Cancer Research at MIT, Love, Kerry R., Shah, Kartik A, Bartlett, Mary Catherine, Leeson, Rachel, Love, John C, Ma, Duanduan, Borowsky, Jonathan, and Wu, Jie

Subjects
0301 basic medicine, Comparative genomics, Computational biology, Biology, biology.organism_classification, Proteomics, Pichia pastoris, Transcriptome, 03 medical and health sciences, 030104 developmental biology, Genetics, Genome Biology, Panomics, DNA microarray, Biotechnology
Abstract

Erratum: In the original publication of this article [1], the accession numbers for the genomes and transcriptome listed are incorrect. The correct details of the NCBI accession numbers can be found below: Availability of data and materials: The genomic sequencing data and assembled and annotated genomes are deposited at NCBI under bioproject accession numbers PRJNA304627 (K. pastoris), PRJNA304977 (K. phaffii wildtype), and PRJNA304976 (K. phaffii GS115). RNA-seq data are deposited at NCBI under the bioproject accession numbers PRJNA311606.

Published
2016

48. Automated pipeline for rapid production & screening of HIV-specific monoclonal antibodies using Pichia pastoris

Author

John J. Clark, J. Christopher Love, Ross M. Zimnisky, Timothy J. Politano, Rachel Leeson, Kerry R. Love, Kartik A. Shah, Nicholas J. Mozdzierz, Brittany A. Goods, Massachusetts Institute of Technology. Center for Biomedical Innovation, Massachusetts Institute of Technology. Department of Chemical Engineering, Koch Institute for Integrative Cancer Research at MIT, Shah, Kartik A, Clark, John J, Goods, Brittany A., Politano, Timothy James, Mozdzierz, Nicholas Joseph, Zimnisky, Ross, Leeson, Rachel, Love, John C, and Love, Kerry R.

Subjects
Time Factors, medicine.drug_class, Human immunodeficiency virus (HIV), Drug Evaluation, Preclinical, Bioengineering, Human pathogen, HIV Antibodies, medicine.disease_cause, Monoclonal antibody, Applied Microbiology and Biotechnology, Article, Pichia, Pichia pastoris, medicine, Humans, Overlap extension polymerase chain reaction, Cloning, biology, Antibodies, Monoclonal, HIV, biology.organism_classification, Virology, Antibodies, Neutralizing, Yeast, Recombinant Proteins, biology.protein, Antibody, Biotechnology
Abstract

Monoclonal antibodies (mAbs) that bind and neutralize human pathogens have great therapeutic potential. Advances in automated screening and liquid handling have resulted in the ability to discover antigen-specific antibodies either directly from human blood or from various combinatorial libraries (phage, bacteria or yeast). There remain, however, bottlenecks in the cloning, expression and evaluation of such lead antibodies identified in primary screens that hinder high-throughput screening. As such, ‘hit-to-lead identification’ remains both expensive and time-consuming. By combining the advantages of overlap extension PCR (OE-PCR) and a genetically stable yet easily manipulatable microbial expression host Pichia pastoris, we have developed an automated pipeline for the rapid production and screening of full-length antigenspecific mAbs. Here, we demonstrate the speed, feasibility and cost-effectiveness of our approach by generating several broadly neutralizing antibodies against human immunodeficiency virus (HIV)., Bill & Melinda Gates Foundation, United States. Defense Advanced Research Projects Agency, Space and Naval Warfare Systems Center San Diego (U.S.) (Contract N66001-13-C-4025), W. M. Keck Foundation, National Institute of Allergy and Infectious Diseases (U.S.) (U19AI090970)., National Cancer Institute (U.S.) (David H. Koch Institute for Integrative Cancer Research at MIT. Support (Core) Grant P30-CA14051)

Published
2015

49. A perfusion-capable microfluidic bioreactor for assessing microbial heterologous protein production

Author

J. Christopher Love, Nicholas J. Mozdzierz, Kartik A. Shah, Rajeev J. Ram, Harry L. T. Lee, Kevin S. Lee, Kerry R. Love, Massachusetts Institute of Technology. Center for Biomedical Innovation, Massachusetts Institute of Technology. Department of Chemical Engineering, Massachusetts Institute of Technology. Research Laboratory of Electronics, Koch Institute for Integrative Cancer Research at MIT, Mozdzierz, Nicholas Joseph, Love, Kerry R., Shah, Kartik A, Ram, Rajeev J, and Love, John C

Subjects
Microfluidics, Biomedical Engineering, Alpha interferon, Heterologous, Bioengineering, Interferon alpha-2, Biochemistry, Pichia, Article, Pichia pastoris, Bioreactors, Bioreactor, Humans, Biomanufacturing, Cells, Cultured, biology, Human Growth Hormone, Interferon-alpha, General Chemistry, Microfluidic Analytical Techniques, biology.organism_classification, Recombinant Proteins, Cell biology, Perfusion, Biochemical engineering
Abstract

We present an integrated microfluidic bioreactor for fully continuous perfusion cultivation of suspended microbial cell cultures. This system allowed continuous and stable heterologous protein expression by sustaining the cultivation of Pichia pastoris over 11 days. This technical capability also allowed testing the impact of perfusion conditions on protein expression. This advance should enable small-scale models for process optimization in continuous biomanufacturing., United States. Defense Advanced Research Projects Agency (N66001-13-C-4025), National Cancer Institute (U.S.) (P30-CA14051), United States. National Institutes of Health (2T32GM008334-26)

Published
2015

50. Engineered SARS-CoV-2 receptor binding domain improves immunogenicity in mice and elicits protective immunity in hamsters.

Author

Dalvie NC, Rodriguez-Aponte SA, Hartwell BL, Tostanoski LH, Biedermann AM, Crowell LE, Kaur K, Kumru O, Carter L, Yu J, Chang A, McMahan K, Courant T, Lebas C, Lemnios AA, Rodrigues KA, Silva M, Johnston RS, Naranjo CA, Tracey MK, Brady JR, Whittaker CA, Yun D, Kar S, Porto M, Lok M, Andersen H, Lewis MG, Love KR, Camp DL, Silverman JM, Kleanthous H, Joshi SB, Volkin DB, Dubois PM, Collin N, King NP, Barouch DH, Irvine DJ, and Love JC

Abstract

Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). 1 Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. 2 Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing costs. 3 These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. 4-6 Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. 7,8 Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge., Competing Interests: Competing interests L.E.C., K.R.L., and J.C.L. have filed patents related to the InSCyT system and methods. N.C.D., S.R.A., and J.C.L. have filed a patent related to the RBD-L452K-F490W sequence. K.R.L., L.E.C., and M.K.T. are current employees at Sunflower Therapeutics PBC. J.C.L. has interests in Sunflower Therapeutics PBC, Pfizer, Honeycomb Biotechnologies, OneCyte Biotechnologies, QuantumCyte, Amgen, and Repligen. J.C.L’s interests are reviewed and managed under MIT’s policies for potential conflicts of interest. J.M.S. is an employee of the Bill & Melinda Gates Medical Research Institute. H.K. is an employee of the Bill & Melinda Gates Foundation.

Published
2021
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