1
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Fang Y, Chang AY, Verma D, Miyashita SI, Eszterhas S, Lee PG, Shen Y, Davis LR, Dong M, Bailey-Kellogg C, Griswold KE. Functional Deimmunization of Botulinum Neurotoxin Protease Domain via Computationally Driven Library Design and Ultrahigh-Throughput Screening. ACS Synth Biol 2023; 12:153-163. [PMID: 36623275 PMCID: PMC9872818 DOI: 10.1021/acssynbio.2c00426] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Indexed: 01/11/2023]
Abstract
Botulinum neurotoxin serotype A (BoNT/A) is a widely used cosmetic agent that also has diverse therapeutic applications; however, adverse antidrug immune responses and associated loss of efficacy have been reported in clinical uses. Here, we describe computational design and ultrahigh-throughput screening of a massive BoNT/A light-chain (BoNT/A-LC) library optimized for reduced T cell epitope content and thereby dampened immunogenicity. We developed a functional assay based on bacterial co-expression of BoNT/A-LC library members with a Förster resonance energy transfer (FRET) sensor for BoNT/A-LC enzymatic activity, and we employed high-speed fluorescence-activated cell sorting (FACS) to identify numerous computationally designed variants having wild-type-like enzyme kinetics. Many of these variants exhibited decreased immunogenicity in humanized HLA transgenic mice and manifested in vivo paralytic activity when incorporated into full-length toxin. One variant achieved near-wild-type paralytic potency and a 300% reduction in antidrug antibody response in vivo. Thus, we have achieved a striking level of BoNT/A-LC functional deimmunization by combining computational library design and ultrahigh-throughput screening. This strategy holds promise for deimmunizing other biologics with complex superstructures and mechanisms of action.
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Affiliation(s)
- Yongliang Fang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Andrew Y. Chang
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Deeptak Verma
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Shin-Ichiro Miyashita
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department
of Food, Aroma and Cosmetic Chemistry, Tokyo
University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan
| | - Susan Eszterhas
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Pyung-Gang Lee
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Yi Shen
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Lydia R. Davis
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Min Dong
- Department
of Urology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Department
of Microbiology and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chris Bailey-Kellogg
- Department
of Computer Science, Dartmouth, Hanover, New Hampshire 03755, United States
| | - Karl E. Griswold
- Thayer
School of Engineering, Dartmouth, Hanover, New Hampshire 03755, United States
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2
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Furlon JM, Mitchell SJ, Bailey-Kellogg C, Griswold KE. Bioinformatics-driven discovery of novel Clostridioides difficile lysins and experimental comparison with highly active benchmarks. Biotechnol Bioeng 2021; 118:2482-2492. [PMID: 33748952 PMCID: PMC10049856 DOI: 10.1002/bit.27759] [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: 12/31/2020] [Revised: 03/07/2021] [Accepted: 03/13/2021] [Indexed: 11/11/2022]
Abstract
Clostridioides difficile is the single most deadly bacterial pathogen in the United States, and its global prevalence and outsized health impacts underscore the need for more effective therapeutic options. Towards this goal, a novel group of modified peptidoglycan hydrolases with significant in vitro bactericidal activity have emerged as potential candidates for treating C. difficile infections (CDI). To date, discovery and development efforts directed at these CDI-specific lysins have been limited, and in particular there has been no systematic comparison of known or newly discovered lysin candidates. Here, we detail bioinformatics-driven discovery of six new anti-C. difficile lysins belonging to the amidase-3 family of enzymes, and we describe experimental comparison of their respective catalytic domains (CATs) with highly active CATs from the literature. Our quantitative analyses include metrics for expression level, inherent antibacterial activity, breadth of strain selectivity, killing of germinating spores, and structural and functional measures of thermal stability. Importantly, prior studies have not examined stability as a performance metric, and our results show that the panel of eight enzymes possess widely variable thermal denaturation temperatures and resistance to heat inactivation, including some enzymes that exhibit marginal stability at body temperature. Ultimately, no single enzyme dominated with respect to all performance measures, suggesting the need for a balanced assessment of lysin properties during efforts to find, engineer, and develop candidates with true clinical potential.
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Affiliation(s)
- Jacob M Furlon
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, USA
| | | | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, USA.,Lyticon LLC, Lebanon, New Hampshire, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, USA.,Lyticon LLC, Lebanon, New Hampshire, USA
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3
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Mitchell SJ, Verma D, Griswold KE, Bailey-Kellogg C. Building blocks and blueprints for bacterial autolysins. PLoS Comput Biol 2021; 17:e1008889. [PMID: 33793553 PMCID: PMC8051824 DOI: 10.1371/journal.pcbi.1008889] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/16/2021] [Accepted: 03/17/2021] [Indexed: 01/31/2023] Open
Abstract
Bacteria utilize a wide variety of endogenous cell wall hydrolases, or autolysins, to remodel their cell walls during processes including cell division, biofilm formation, and programmed death. We here systematically investigate the composition of these enzymes in order to gain insights into their associated biological processes, potential ways to disrupt them via chemotherapeutics, and strategies by which they might be leveraged as recombinant antibacterial biotherapies. To do so, we developed LEDGOs (lytic enzyme domains grouped by organism), a pipeline to create and analyze databases of autolytic enzyme sequences, constituent domain annotations, and architectural patterns of multi-domain enzymes that integrate peptidoglycan binding and degrading functions. We applied LEDGOs to eight pathogenic bacteria, gram negatives Acinetobacter baumannii, Klebsiella pneumoniae, Neisseria gonorrhoeae, and Pseudomonas aeruginosa; and gram positives Clostridioides difficile, Enterococcus faecium, Staphylococcus aureus, and Streptococcus pneumoniae. Our analysis of the autolytic enzyme repertoires of these pathogens reveals commonalities and differences in their key domain building blocks and architectures, including correlations and preferred orders among domains in multi-domain enzymes, repetitions of homologous binding domains with potentially complementarity recognition modalities, and sequence similarity patterns indicative of potential divergence of functional specificity among related domains. We have further identified a variety of unannotated sequence regions within the lytic enzymes that may themselves contain new domains with important functions.
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Affiliation(s)
- Spencer J. Mitchell
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
| | - Deeptak Verma
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America
- Lyticon LLC, Lebanon, New Hampshire, United States of America
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
- Lyticon LLC, Lebanon, New Hampshire, United States of America
- * E-mail:
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4
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Blumenthal I, Davis LR, Berman CM, Griswold KE. Nonclassical antagonism between human lysozyme and AMPs against Pseudomonas aeruginosa. FEBS Open Bio 2021; 11:705-713. [PMID: 33480189 PMCID: PMC7931236 DOI: 10.1002/2211-5463.13094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/25/2020] [Accepted: 01/14/2021] [Indexed: 12/28/2022] Open
Abstract
Combinations of human lysozyme (hLYS) and antimicrobial peptides (AMPs) are known to exhibit either additive or synergistic activity, and as a result, they have therapeutic potential for persistent and antibiotic‐resistant infections. We examined hLYS activity against Pseudomonas aeruginosa when combined with six different AMPs. In contrast to prior reports, we discovered that some therapeutically relevant AMPs manifest striking antagonistic interactions with hLYS across particular concentration ranges. We further found that the synthetic AMP Tet009 can inhibit hLYS‐mediated bacterial lysis. To the best of our knowledge, these results represent the first observations of antagonism between hLYS and AMPs, and they advise that future development of lytic enzyme and AMP combination therapies considers the potential for antagonistic interactions.
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Affiliation(s)
- Ian Blumenthal
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Lydia R Davis
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Chet M Berman
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA.,Lyticon LLC, Lebanon, NH, USA
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5
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Zhao H, Brooks SA, Eszterhas S, Heim S, Li L, Xiong YQ, Fang Y, Kirsch JR, Verma D, Bailey-Kellogg C, Griswold KE. Globally deimmunized lysostaphin evades human immune surveillance and enables highly efficacious repeat dosing. Sci Adv 2020; 6:6/36/eabb9011. [PMID: 32917596 PMCID: PMC7467700 DOI: 10.1126/sciadv.abb9011] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/21/2020] [Indexed: 06/11/2023]
Abstract
There is a critical need for novel therapies to treat methicillin-resistant Staphylococcus aureus (MRSA) and other drug-resistant pathogens, and lysins are among the vanguard of innovative antibiotics under development. Unfortunately, lysins' own microbial origins can elicit detrimental antidrug antibodies (ADAs) that undermine efficacy and threaten patient safety. To create an enhanced anti-MRSA lysin, a novel variant of lysostaphin was engineered by T cell epitope deletion. This "deimmunized" lysostaphin dampened human T cell activation, mitigated ADA responses in human HLA transgenic mice, and enabled safe and efficacious repeated dosing during a 6-week longitudinal infection study. Furthermore, the deimmunized lysostaphin evaded established anti-wild-type immunity, thereby providing significant anti-MRSA protection for animals that were immune experienced to the wild-type enzyme. Last, the enzyme synergized with daptomycin to clear a stringent model of MRSA endocarditis. By mitigating T cell-driven antidrug immunity, deimmunized lysostaphin may enable safe, repeated dosing to treat refractory MRSA infections.
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Affiliation(s)
- Hongliang Zhao
- Thayer School of Engineering, Dartmouth, Hanover, NH 03755, USA
| | - Seth A Brooks
- Thayer School of Engineering, Dartmouth, Hanover, NH 03755, USA
| | - Susan Eszterhas
- Thayer School of Engineering, Dartmouth, Hanover, NH 03755, USA
| | - Spencer Heim
- Thayer School of Engineering, Dartmouth, Hanover, NH 03755, USA
| | - Liang Li
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yan Q Xiong
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yongliang Fang
- Thayer School of Engineering, Dartmouth, Hanover, NH 03755, USA
- Lyticon LLC, Lebanon, NH 03766, USA
| | - Jack R Kirsch
- Thayer School of Engineering, Dartmouth, Hanover, NH 03755, USA
| | - Deeptak Verma
- Department of Computer Science, Dartmouth, Hanover, NH 03755, USA
| | - Chris Bailey-Kellogg
- Lyticon LLC, Lebanon, NH 03766, USA
- Department of Computer Science, Dartmouth, Hanover, NH 03755, USA
- Stealth Biologics LLC, Lebanon, NH 03766, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH 03755, USA.
- Lyticon LLC, Lebanon, NH 03766, USA
- Stealth Biologics LLC, Lebanon, NH 03766, USA
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6
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Choi Y, Jeong S, Choi JM, Ndong C, Griswold KE, Bailey-Kellogg C, Kim HS. Computer-guided binding mode identification and affinity improvement of an LRR protein binder without structure determination. PLoS Comput Biol 2020; 16:e1008150. [PMID: 32866140 PMCID: PMC7485979 DOI: 10.1371/journal.pcbi.1008150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 09/11/2020] [Accepted: 07/14/2020] [Indexed: 12/24/2022] Open
Abstract
Precise binding mode identification and subsequent affinity improvement without structure determination remain a challenge in the development of therapeutic proteins. However, relevant experimental techniques are generally quite costly, and purely computational methods have been unreliable. Here, we show that integrated computational and experimental epitope localization followed by full-atom energy minimization can yield an accurate complex model structure which ultimately enables effective affinity improvement and redesign of binding specificity. As proof-of-concept, we used a leucine-rich repeat (LRR) protein binder, called a repebody (Rb), that specifically recognizes human IgG1 (hIgG1). We performed computationally-guided identification of the Rb:hIgG1 binding mode and leveraged the resulting model to reengineer the Rb so as to significantly increase its binding affinity for hIgG1 as well as redesign its specificity toward multiple IgGs from other species. Experimental structure determination verified that our Rb:hIgG1 model closely matched the co-crystal structure. Using a benchmark of other LRR protein complexes, we further demonstrated that the present approach may be broadly applicable to proteins undergoing relatively small conformational changes upon target binding.
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Affiliation(s)
- Yoonjoo Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Sukyo Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Jung-Min Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Christian Ndong
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
- Norris Cotton Cancer Center at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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7
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Lai JI, Eszterhas SK, Brooks SA, Guo C, Zolla-Pazner S, Seaman MS, Bailey-Kellogg C, Griswold KE, Ackerman ME. Induction of cross-reactive HIV-1 specific antibody responses by engineered V1V2 immunogens with reduced conformational plasticity. Vaccine 2020; 38:3436-3446. [PMID: 32192810 PMCID: PMC7132531 DOI: 10.1016/j.vaccine.2020.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/26/2020] [Accepted: 03/03/2020] [Indexed: 01/13/2023]
Abstract
Antibodies against the HIV-1 V1V2 loops were the only correlate of reduced infection risk in the RV144 vaccine trial, highlighting the V1V2 loops as promising targets for vaccine design. The V1V2 loops are structurally plastic, exhibiting either an α-helix-coil or β-strand conformation. V1V2-specific antibodies may thus recognize distinct conformations, and an antibody's conformational specificity can be an important determinant of breadth and function. Restricting V1V2 conformational plasticity in an immunogen may thus provide control over the conformational specificity and quality of a vaccine-elicited antibody response. Previously, we identified a V1V2 sequence variant (K155M) that results in enhanced recognition by cross-reactive antibodies recognizing the β-strand conformation. Here, we relate V1V2 antigenicity to immunogenicity by comparing the immunogenicity profiles of wildtype and K155M immunogens in two mouse models. In one model, immunization with gp70 V1V2 K155M but not wildtype elicited antibody responses that were cross-reactive to a panel of heterologous gp120 and gp140 antigens. In a second model, we compared the effect of K155M on immunogenicity in the context of gp70 V1V2, gD V1V2 and gp120, examining the effects of scaffold, epitope-focusing and immunization regimen. K155M variants, especially in the context of a gp120 immunogen, resulted in more robust, durable and cross-reactive antibody responses than wildtype immunogens. Restriction of the β-stranded V1V2 conformation in K155M immunogens may thus be associated with the induction of cross-reactive antibody responses thought to be required of a protective HIV-1 vaccine.
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Affiliation(s)
- Jennifer I Lai
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | | | - Seth A Brooks
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Chengzi Guo
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Susan Zolla-Pazner
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Karl E Griswold
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA; Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
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8
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Choi Y, Furlon JM, Amos RB, Griswold KE, Bailey-Kellogg C. DisruPPI: structure-based computational redesign algorithm for protein binding disruption. Bioinformatics 2019; 34:i245-i253. [PMID: 29949961 PMCID: PMC6022686 DOI: 10.1093/bioinformatics/bty274] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Motivation Disruption of protein–protein interactions can mitigate antibody recognition of therapeutic proteins, yield monomeric forms of oligomeric proteins, and elucidate signaling mechanisms, among other applications. While designing affinity-enhancing mutations remains generally quite challenging, both statistically and physically based computational methods can precisely identify affinity-reducing mutations. In order to leverage this ability to design variants of a target protein with disrupted interactions, we developed the DisruPPI protein design method (DISRUpting Protein–Protein Interactions) to optimize combinations of mutations simultaneously for both disruption and stability, so that incorporated disruptive mutations do not inadvertently affect the target protein adversely. Results Two existing methods for predicting mutational effects on binding, FoldX and INT5, were demonstrated to be quite precise in selecting disruptive mutations from the SKEMPI and AB-Bind databases of experimentally determined changes in binding free energy. DisruPPI was implemented to use an INT5-based disruption score integrated with an AMBER-based stability assessment and was applied to disrupt protein interactions in a set of different targets representing diverse applications. In retrospective evaluation with three different case studies, comparison of DisruPPI-designed variants to published experimental data showed that DisruPPI was able to identify more diverse interaction-disrupting and stability-preserving variants more efficiently and effectively than previous approaches. In prospective application to an interaction between enhanced green fluorescent protein (EGFP) and a nanobody, DisruPPI was used to design five EGFP variants, all of which were shown to have significantly reduced nanobody binding while maintaining function and thermostability. This demonstrates that DisruPPI may be readily utilized for effective removal of known epitopes of therapeutically relevant proteins. Availability and implementation DisruPPI is implemented in the EpiSweep package, freely available under an academic use license. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yoonjoo Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jacob M Furlon
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Ryan B Amos
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA.,Norris Cotton Cancer Center at Dartmouth, Lebanon, NH, USA.,Department of Biological Sciences, Dartmouth, Hanover, NH, USA
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9
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Scanlon TC, Dostal SM, Griswold KE. Erratum for "A high-throughput screen for antibiotic drug discovery" (Volume 111, issue 2, pp. 232-243). Biotechnol Bioeng 2018; 116:475. [PMID: 31290638 DOI: 10.1002/bit.26840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Bricio-Moreno L, Sheridan VH, Goodhead I, Armstrong S, Wong JKL, Waters EM, Sarsby J, Panagiotou S, Dunn J, Chakraborty A, Fang Y, Griswold KE, Winstanley C, Fothergill JL, Kadioglu A, Neill DR. Evolutionary trade-offs associated with loss of PmrB function in host-adapted Pseudomonas aeruginosa. Nat Commun 2018; 9:2635. [PMID: 29980663 PMCID: PMC6035264 DOI: 10.1038/s41467-018-04996-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 06/06/2018] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas aeruginosa colonises the upper airway of cystic fibrosis (CF) patients, providing a reservoir of host-adapted genotypes that subsequently establish chronic lung infection. We previously experimentally-evolved P. aeruginosa in a murine model of respiratory tract infection and observed early-acquired mutations in pmrB, encoding the sensor kinase of a two-component system that promoted establishment and persistence of infection. Here, using proteomics, we show downregulation of proteins involved in LPS biosynthesis, antimicrobial resistance and phenazine production in pmrB mutants, and upregulation of proteins involved in adherence, lysozyme resistance and inhibition of the chloride ion channel CFTR, relative to wild-type strain LESB65. Accordingly, pmrB mutants are susceptible to antibiotic treatment but show enhanced adherence to airway epithelial cells, resistance to lysozyme treatment, and downregulate host CFTR expression. We propose that P. aeruginosa pmrB mutations in CF patients are subject to an evolutionary trade-off, leading to enhanced colonisation potential, CFTR inhibition, and resistance to host defences, but also to increased susceptibility to antibiotics.
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Affiliation(s)
- Laura Bricio-Moreno
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Victoria H Sheridan
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Ian Goodhead
- School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
| | - Stuart Armstrong
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 3GL, UK
| | - Janet K L Wong
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Elaine M Waters
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
- Department of Microbiology, School of Natural Science, National University of Ireland, Galway, H91 TK33, Ireland
| | - Joscelyn Sarsby
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Stavros Panagiotou
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - James Dunn
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Adrita Chakraborty
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Yongliang Fang
- Thayer School of Engineering, Dartmouth, Hanover, NH, 03755, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, 03755, USA
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK.
| | - Aras Kadioglu
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK
| | - Daniel R Neill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, L69 7BE, UK.
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11
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Broadway PR, Carroll JA, Burdick Sanchez NC, Callaway TR, Lawhon SD, Bryan LK, Gart EV, Hughes HD, Hergenreder JE, Rounds PW, Griswold KE. 79 The Effects of the Dfm Clostat® and Experimental Salmonella Challenge on the Microbiome of the Ileum in Weaned Holstein Steer Calves. J Anim Sci 2018. [DOI: 10.1093/jas/sky027.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- P R Broadway
- USDA-ARS, Livestock Issues Research Unit, Lubbock, TX
| | - J A Carroll
- USDA-ARS, Livestock Issues Research Unit, Lubbock, TX
| | | | - T R Callaway
- University of Georgia, Department of Animal and Dairy Science, Athens, GA
| | - S D Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX
| | - L K Bryan
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX
| | - E V Gart
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX
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12
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Abstract
Gel microdroplet – fluorescence activated cell sorting (GMD-FACS) is an innovative high throughput screening platform for recombinant protein libraries, and we show here that GMD-FACS can overcome many of the limitations associated with conventional screening methods for antibody libraries. For example, phage and cell surface display benefit from exceptionally high throughput, but generally require high quality, soluble antigen target and necessitate the use of anchored antibody fragments. In contrast, the GMD-FACS assay can screen for soluble, secreted, full-length IgGs at rates of several thousand clones per second, and the technique enables direct screening against membrane protein targets in their native cellular context. In proof-of-concept experiments, rare anti-EGFR antibody clones were efficiently enriched from a 10,000-fold excess of anti-CCR5 clones in just three days. Looking forward, GMD-FACS has the potential to contribute to antibody discovery and engineering for difficult targets, such as ion channels and G protein-coupled receptors.
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Affiliation(s)
- Yongliang Fang
- a Thayer School of Engineering, Dartmouth , Hanover , NH , USA
| | - Thach H Chu
- a Thayer School of Engineering, Dartmouth , Hanover , NH , USA
| | - Margaret E Ackerman
- a Thayer School of Engineering, Dartmouth , Hanover , NH , USA.,b Department of Microbiology and Immunology , Dartmouth , Hanover , NH , USA
| | - Karl E Griswold
- a Thayer School of Engineering, Dartmouth , Hanover , NH , USA.,c Immunology & Cancer Immunotherapy Program, Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center , Lebanon , NH , USA.,d Department of Biological Sciences , Dartmouth , Hanover , NH.,e Department of Chemistry , Dartmouth , Hanover , NH , USA
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13
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Ficko BW, NDong C, Giacometti P, Griswold KE, Diamond SG. A Feasibility Study of Nonlinear Spectroscopic Measurement of Magnetic Nanoparticles Targeted to Cancer Cells. IEEE Trans Biomed Eng 2016; 64:972-979. [PMID: 27352362 DOI: 10.1109/tbme.2016.2584241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Magnetic nanoparticles (MNPs) are an emerging platform for targeted diagnostics in cancer. An important component needed for translation of MNPs is the detection and quantification of targeted MNPs bound to tumor cells. METHOD This study explores the feasibility of a multifrequency nonlinear magnetic spectroscopic method that uses excitation and pickup coils and is capable of discriminating between quantities of bound and unbound MNPs in 0.5 ml samples of KB and Igrov human cancer cell lines. The method is tested over a range of five concentrations of MNPs from 0 to 80 μg/ml and five concentrations of cells from 50 to 400 000 count per ml. RESULTS A linear model applied to the magnetic spectroscopy data was able to simultaneously measure bound and unbound MNPs with agreement between the model-fit and lab assay measurements (p < 0.001). The detectable iron of the presented method to bound and unbound MNPs was < 2 μg in a 0.5 ml sample. The linear model parameters used to determine the quantities of bound and unbound nanoparticles in KB cells were also used to measure the bound and unbound MNP in the Igrov cell line and vice versa. CONCLUSION Nonlinear spectroscopic measurement of MNPs may be a useful method for studying targeted MNPs in oncology. SIGNIFICANCE Determining the quantity of bound and unbound MNP in an unknown sample using a linear model represents an exciting opportunity to translate multifrequency nonlinear spectroscopy methods to in vivo applications where MNPs could be targeted to cancer cells.
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14
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Choi Y, Ndong C, Griswold KE, Bailey-Kellogg C. Computationally driven antibody engineering enables simultaneous humanization and thermostabilization. Protein Eng Des Sel 2016; 29:419-426. [PMID: 27334453 DOI: 10.1093/protein/gzw024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 02/08/2016] [Accepted: 05/25/2016] [Indexed: 12/22/2022] Open
Abstract
Humanization reduces the immunogenicity risk of therapeutic antibodies of non-human origin. Thermostabilization can be critical for clinical development and application of therapeutic antibodies. Here, we show that the computational antibody redesign method Computationally Driven Antibody Humanization (CoDAH) enables these two goals to be accomplished simultaneously and seamlessly. A panel of CoDAH designs for the murine parent of cetuximab, a chimeric anti-EGFR antibody, exhibited both substantially improved thermostabilities and substantially higher levels of humanness, while retaining binding activity near the parental level. The consistently high quality of the turnkey CoDAH designs, over a whole panel of variants, suggests that the computationally directed approach encapsulates key determinants of antibody structure and function.
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Affiliation(s)
- Yoonjoo Choi
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
| | - Christian Ndong
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA.,Norris Cotton Cancer Center at Dartmouth, Lebanon, NH 03766, USA.,Department of Biological Sciences, Dartmouth, Hanover, NH 03755, USA
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15
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Griswold KE, Bailey-Kellogg C. Design and engineering of deimmunized biotherapeutics. Curr Opin Struct Biol 2016; 39:79-88. [PMID: 27322891 DOI: 10.1016/j.sbi.2016.06.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 12/26/2022]
Abstract
Therapeutic proteins are powerful next-generation drugs able to effectively treat diverse and devastating diseases, but the development and use of biotherapeutics entails unique challenges and risks. In particular, protein drugs are subject to immune surveillance in the human body, and ensuing antidrug immune responses can cause a wide range of problems including altered pharmacokinetics, loss of efficacy, and even life-threating complications. Here we review recent progress in technologies for engineering deimmunized biotherapeutics, placing particular emphasis on deletion of immunogenic antibody and T cell epitopes via experimentally or computationally guided mutagenesis.
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Affiliation(s)
- Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, United States; Stealth Biologics LLC, Lyme, NH, United States.
| | - Chris Bailey-Kellogg
- Stealth Biologics LLC, Lyme, NH, United States; Department of Computer Science, Dartmouth, Hanover, NH, United States.
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16
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Zhao H, Verma D, Li W, Choi Y, Ndong C, Fiering SN, Bailey-Kellogg C, Griswold KE. Depletion of T cell epitopes in lysostaphin mitigates anti-drug antibody response and enhances antibacterial efficacy in vivo. ACTA ACUST UNITED AC 2016; 22:629-39. [PMID: 26000749 DOI: 10.1016/j.chembiol.2015.04.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 01/17/2023]
Abstract
The enzyme lysostaphin possesses potent anti-staphylococcal activity and represents a promising antibacterial drug candidate; however, its immunogenicity poses a barrier to clinical translation. Here, structure-based biomolecular design enabled widespread depletion of lysostaphin DRB1(∗)0401 restricted T cell epitopes, and resulting deimmunized variants exhibited striking reductions in anti-drug antibody responses upon administration to humanized HLA-transgenic mice. This reduced immunogenicity translated into improved efficacy in the form of protection against repeated challenges with methicillin-resistant Staphylococcus aureus (MRSA). In contrast, while wild-type lysostaphin was efficacious against the initial MRSA infection, it failed to clear subsequent bacterial challenges that were coincident with escalating anti-drug antibody titers. These results extend the existing deimmunization literature, in which reduced immunogenicity and retained efficacy are assessed independently of each other. By correlating in vivo efficacy with longitudinal measures of anti-drug antibody development, we provide the first direct evidence that T cell epitope depletion manifests enhanced biotherapeutic efficacy.
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Affiliation(s)
- Hongliang Zhao
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH 03755, USA; Laboratory of Microorganism Engineering, Beijing Institute of Biotechnology, 20 Dongdajie Street, Fengtai District, Beijing 100071, People's Republic of China
| | - Deeptak Verma
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA
| | - Wen Li
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA
| | - Christian Ndong
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Steven N Fiering
- Department of Microbiology and Immunology, Dartmouth, Hanover, NH 03755, USA; Norris Cotton Cancer Center at Dartmouth, Lebanon, NH 03766, USA
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, NH 03755, USA.
| | - Karl E Griswold
- Thayer School of Engineering at Dartmouth, 14 Engineering Drive, Hanover, NH 03755, USA; Norris Cotton Cancer Center at Dartmouth, Lebanon, NH 03766, USA; Department of Biological Sciences, Dartmouth, Hanover, NH 03755, USA.
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17
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Funaro MG, Nemani KV, Chen Z, Bhujwalla ZM, Griswold KE, Gimi B. Effect of alginate microencapsulation on the catalytic efficiency andin vitroenzyme-prodrug therapeutic efficacy of cytosine deaminase and of recombinantE. coliexpressing cytosine deaminase. J Microencapsul 2015; 33:64-70. [DOI: 10.3109/02652048.2015.1115902] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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18
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Salvat RS, Choi Y, Bishop A, Bailey-Kellogg C, Griswold KE. Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads. Biotechnol Bioeng 2015; 112:1306-18. [PMID: 25655032 PMCID: PMC4452428 DOI: 10.1002/bit.25554] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 01/09/2015] [Accepted: 01/18/2015] [Indexed: 12/31/2022]
Abstract
Anti-drug immune responses are a unique risk factor for biotherapeutics, and undesired immunogenicity can alter pharmacokinetics, compromise drug efficacy, and in some cases even threaten patient safety. To fully capitalize on the promise of biotherapeutics, more efficient and generally applicable protein deimmunization tools are needed. Mutagenic deletion of a protein's T cell epitopes is one powerful strategy to engineer immunotolerance, but deimmunizing mutations must maintain protein structure and function. Here, EpiSweep, a structure-based protein design and deimmunization algorithm, has been used to produce a panel of seven beta-lactamase drug candidates having 27-47% reductions in predicted epitope content. Despite bearing eight mutations each, all seven engineered enzymes maintained good stability and activity. At the same time, the variants exhibited dramatically reduced interaction with human class II major histocompatibility complex proteins, key regulators of anti-drug immune responses. When compared to 8-mutation designs generated with a sequence-based deimmunization algorithm, the structure-based designs retained greater thermostability and possessed fewer high affinity epitopes, the dominant drivers of anti-biotherapeutic immune responses. These experimental results validate the first structure-based deimmunization algorithm capable of mapping optimal biotherapeutic design space. By designing optimal mutations that reduce immunogenic potential while imparting favorable intramolecular interactions, broadly distributed epitopes may be simultaneously targeted using high mutational loads.
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Affiliation(s)
- Regina S Salvat
- Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755
| | | | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755.
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755.
- Program in Molecular and Cellular Biology, Dartmouth, Hanover, New Hampshire.
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19
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Blazanovic K, Zhao H, Choi Y, Li W, Salvat RS, Osipovitch DC, Fields J, Moise L, Berwin BL, Fiering SN, Bailey-Kellogg C, Griswold KE. Structure-based redesign of lysostaphin yields potent antistaphylococcal enzymes that evade immune cell surveillance. Mol Ther Methods Clin Dev 2015; 2:15021. [PMID: 26151066 PMCID: PMC4470366 DOI: 10.1038/mtm.2015.21] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 12/22/2022]
Abstract
Staphylococcus aureus infections exert a tremendous burden on the health-care system, and the threat of drug-resistant strains continues to grow. The bacteriolytic enzyme lysostaphin is a potent antistaphylococcal agent with proven efficacy against both drug-sensitive and drug-resistant strains; however, the enzyme's own bacterial origins cause undesirable immunogenicity and pose a barrier to clinical translation. Here, we deimmunized lysostaphin using a computationally guided process that optimizes sets of mutations to delete immunogenic T cell epitopes without disrupting protein function. In vitro analyses showed the methods to be both efficient and effective, producing seven different deimmunized designs exhibiting high function and reduced immunogenic potential. Two deimmunized candidates elicited greatly suppressed proliferative responses in splenocytes from humanized mice, while at the same time the variants maintained wild-type efficacy in a staphylococcal pneumonia model. Overall, the deimmunized enzymes represent promising leads in the battle against S. aureus.
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Affiliation(s)
| | - Hongliang Zhao
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA ; Laboratory of Microorganism Engineering, Beijing Institute of Biotechnology , Beijing, People's Republic of China
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth , Hanover, New Hampshire, USA
| | - Wen Li
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA
| | - Regina S Salvat
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA
| | - Daniel C Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth , Hanover, New Hampshire, USA
| | - Jennifer Fields
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA
| | - Leonard Moise
- Institute for Immunology and Informatics, University of Rhode Island , Providence, Rhode Island, USA
| | - Brent L Berwin
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA
| | - Steven N Fiering
- Department of Microbiology and Immunology, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA
| | | | - Karl E Griswold
- Thayer School of Engineering, Dartmouth , Hanover, New Hampshire, USA ; Norris Cotton Cancer Center, Dartmouth , Hanover, New Hampshire, USA ; Department of Biological Sciences, Dartmouth , Hanover, New Hampshire, USA
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20
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Dostal SM, Fang Y, Guerrette JC, Scanlon TC, Griswold KE. Genetically enhanced lysozyme evades a pathogen derived inhibitory protein. ACS Chem Biol 2015; 10:1110-7. [PMID: 25607237 DOI: 10.1021/cb500976y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The accelerating spread of drug-resistant bacteria is creating demand for novel antibiotics. Bactericidal enzymes, such as human lysozyme (hLYZ), are interesting drug candidates due to their inherent catalytic nature and lack of susceptibility to the resistance mechanisms typically directed toward chemotherapeutics. However, natural antibacterial enzymes have their own limitations. For example, hLYZ is susceptible to pathogen derived inhibitory proteins, such as Escherichia coli Ivy. Here, we describe proof of concept studies demonstrating that hLYZ can be effectively redesigned to evade this potent lysozyme inhibitor. Large combinatorial libraries of hLYZ were analyzed using an innovative screening platform based on microbial coculture in hydrogel microdroplets. Isolated hLYZ variants were orders of magnitude less susceptible to E. coli Ivy yet retained high catalytic proficiency and inherent antibacterial activity. Interestingly, the engineered escape variants showed a disadvantageous increase in susceptibility to the related Ivy ortholog from Pseudomonas aeruginosa as well as an unrelated E. coli inhibitory protein, MliC. Thus, while we have achieved our original objective with respect to escaping E. coli Ivy, engineering hLYZ for broad-spectrum evasion of proteinaceous inhibitors will require consideration of the complex and varied determinants that underlie molecular recognition by these emerging virulence factors.
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Affiliation(s)
- Sarah M. Dostal
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
| | - Yongliang Fang
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
| | - Jonathan C. Guerrette
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
| | - Thomas C. Scanlon
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
| | - Karl E. Griswold
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, New Hampshire 03755, United States
- Program in Molecular and Cellular Biology, Dartmouth College, Hanover, New Hampshire 03755, United States
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21
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Ndong C, Toraya-Brown S, Kekalo K, Baker I, Gerngross TU, Fiering SN, Griswold KE. Antibody-mediated targeting of iron oxide nanoparticles to the folate receptor alpha increases tumor cell association in vitro and in vivo. Int J Nanomedicine 2015; 10:2595-617. [PMID: 25878495 PMCID: PMC4388088 DOI: 10.2147/ijn.s79367] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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] [Indexed: 11/23/2022] Open
Abstract
Active molecular targeting has become an important aspect of nanoparticle development for oncology indications. Here, we describe molecular targeting of iron oxide nanoparticles (IONPs) to the folate receptor alpha (FOLRα) using an engineered antibody fragment (Ffab). Compared to control nanoparticles targeting the non-relevant botulinum toxin, the Ffab-IONP constructs selectively accumulated on FOLRα-overexpressing cancer cells in vitro, where they exhibited the capacity to internalize into intracellular vesicles. Similarly, Ffab-IONPs homed to FOLRα-positive tumors upon intraperitoneal administration in an orthotopic murine xenograft model of ovarian cancer, whereas negative control particles showed no detectable tumor accumulation. Interestingly, Ffab-IONPs built with custom 120 nm nanoparticles exhibited lower in vitro targeting efficiency when compared to those built with commercially sourced 180 nm nanoparticles. In vivo, however, the two Ffab-IONP platforms achieved equivalent tumor homing, although the smaller 120 nm IONPs were more prone to liver sequestration. Overall, the results show that Ffab-mediated targeting of IONPs yields specific, high-level accumulation within cancer cells, and this fact suggests that Ffab-IONPs could have future utility in ovarian cancer diagnostics and therapy.
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Affiliation(s)
| | - Seiko Toraya-Brown
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | | | - Ian Baker
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Tillman U Gerngross
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA ; Department of Biological Sciences, Dartmouth, Hanover, NH, USA ; Department of Chemistry, Dartmouth, Hanover, NH, USA
| | - Steven N Fiering
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA ; Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA ; Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA ; Department of Biological Sciences, Dartmouth, Hanover, NH, USA ; Norris Cotton Cancer Center, Lebanon, NH, USA
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22
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Nemani KV, Ennis RC, Griswold KE, Gimi B. Magnetic nanoparticle hyperthermia induced cytosine deaminase expression in microencapsulated E. coli for enzyme-prodrug therapy. J Biotechnol 2015; 203:32-40. [PMID: 25820125 DOI: 10.1016/j.jbiotec.2015.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 08/20/2014] [Revised: 03/10/2015] [Accepted: 03/16/2015] [Indexed: 11/17/2022]
Abstract
Engineered bacterial cells that are designed to express therapeutic enzymes under the transcriptional control of remotely inducible promoters can mediate the de novo conversion of non-toxic prodrugs to their cytotoxic forms. In situ cellular expression of enzymes provides increased stability and control of enzyme activity as compared to isolated enzymes. We have engineered Escherichia coli (E. coli), designed to express cytosine deaminase at elevated temperatures, under the transcriptional control of thermo-regulatory λpL-cI857 promoter cassette which provides a thermal switch to trigger enzyme synthesis. Enhanced cytosine deaminase expression was observed in cultures incubated at 42°C as compared to 30°C, and enzyme expression was further substantiated by spectrophotometric assays indicating enhanced conversion of 5-fluorocytosine to 5-fluorouracil. The engineered cells were subsequently co-encapsulated with magnetic iron oxide nanoparticles in immunoprotective alginate microcapsules, and cytosine deaminase expression was triggered remotely by alternating magnetic field-induced hyperthermia. The combination of 5-fluorocytosine with AMF-activated microcapsules demonstrated tumor cell cytotoxicity comparable to direct treatment with 5-fluorouracil chemotherapy. Such enzyme-prodrug therapy, based on engineered and immunoisolated E. coli, may ultimately yield an improved therapeutic index relative to monotherapy, as AMF mediated hyperthermia might be expected to pre-sensitize tumors to chemotherapy under appropriate conditions.
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Affiliation(s)
| | | | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA; Department of Biological Sciences, Dartmouth, Hanover, NH, USA; Program in Molecular and Cellular Biology, Dartmouth, Hanover, NH, USA
| | - Barjor Gimi
- Department of Radiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Thayer School of Engineering, Dartmouth, Hanover, NH, USA; Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
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23
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NDong C, Tate JA, Kett WC, Batra J, Demidenko E, Lewis LD, Hoopes PJ, Gerngross TU, Griswold KE. Tumor cell targeting by iron oxide nanoparticles is dominated by different factors in vitro versus in vivo. PLoS One 2015; 10:e0115636. [PMID: 25695795 PMCID: PMC4335054 DOI: 10.1371/journal.pone.0115636] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/25/2014] [Indexed: 11/29/2022] Open
Abstract
Realizing the full potential of iron oxide nanoparticles (IONP) for cancer diagnosis and therapy requires selective tumor cell accumulation. Here, we report a systematic analysis of two key determinants for IONP homing to human breast cancers: (i) particle size and (ii) active vs passive targeting. In vitro, molecular targeting to the HER2 receptor was the dominant factor driving cancer cell association. In contrast, size was found to be the key determinant of tumor accumulation in vivo, where molecular targeting increased tumor tissue concentrations for 30 nm but not 100 nm IONP. Similar to the in vitro results, PEGylation did not influence in vivo IONP biodistribution. Thus, the results reported here indicate that the in vitro advantages of molecular targeting may not consistently extend to pre-clinical in vivo settings. These observations may have important implications for the design and clinical translation of advanced, multifunctional, IONP platforms.
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Affiliation(s)
- Christian NDong
- Thayer School of Engineering, Dartmouth, Hanover, NH, United States of America
| | - Jennifer A. Tate
- Thayer School of Engineering, Dartmouth, Hanover, NH, United States of America
| | - Warren C. Kett
- Thayer School of Engineering, Dartmouth, Hanover, NH, United States of America
| | - Jaya Batra
- Thayer School of Engineering, Dartmouth, Hanover, NH, United States of America
| | - Eugene Demidenko
- Department of Biostatistics and Medicine, The Geisel School of Medicine at Dartmouth, Lebanon, NH, United States of America
| | - Lionel D. Lewis
- Department of Biostatistics and Medicine, The Geisel School of Medicine at Dartmouth, Lebanon, NH, United States of America
| | - P. Jack Hoopes
- Department of Biostatistics and Medicine, The Geisel School of Medicine at Dartmouth, Lebanon, NH, United States of America
| | - Tillman U. Gerngross
- Thayer School of Engineering, Dartmouth, Hanover, NH, United States of America
- Department of Biological Sciences, Dartmouth, Hanover, NH, United States of America
- Department of Chemistry, Dartmouth, Hanover, NH, United States of America
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, United States of America
- Program in Molecular and Cellular Biology, Dartmouth, Hanover, NH, United States of America
- Department of Biological Sciences, Dartmouth, Hanover, NH, United States of America
- * E-mail:
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24
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Osipovitch DC, Therrien S, Griswold KE. Discovery of novel S. aureus autolysins and molecular engineering to enhance bacteriolytic activity. Appl Microbiol Biotechnol 2015; 99:6315-26. [PMID: 25690309 DOI: 10.1007/s00253-015-6443-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/24/2015] [Accepted: 01/26/2015] [Indexed: 01/21/2023]
Abstract
Staphylococcus aureus is a dangerous bacterial pathogen whose clinical impact has been amplified by the emergence and rapid spread of antibiotic resistance. In the search for more effective therapeutic strategies, great effort has been placed on the study and development of staphylolytic enzymes, which benefit from high potency activity toward drug-resistant strains, and a low inherent susceptibility to emergence of new resistance phenotypes. To date, the majority of therapeutic candidates have derived from either bacteriophage or environmental competitors of S. aureus. Little to no consideration has been given to cis-acting autolysins that represent key elements in the bacterium's endogenous cell wall maintenance and recycling machinery. In this study, five putative autolysins were cloned from the S. aureus genome, and their activities were evaluated. Four of these novel enzymes, or component domains thereof, demonstrated lytic activity toward live S. aureus cells, but their potencies were 10s to 1000s of times lower than that of the well-characterized therapeutic candidate lysostaphin. We hypothesized that their poor activities were due in part to suboptimal cell wall targeting associated with their native cell wall binding domains, and we sought to enhance their antibacterial potential via chimeragenesis with the peptidoglycan binding domain of lysostaphin. The most potent chimera exhibited a 140-fold increase in lytic rate, bringing it within 8-fold of lysostaphin. While this enzyme was sensitive to certain biologically relevant environmental factors and failed to exhibit a measurable minimal inhibitory concentration, it was able to kill lysostaphin-resistant S. aureus and ultimately proved active in lung surfactant. We conclude that the S. aureus proteome represents a rich and untapped reservoir of novel antibacterial enzymes, and we demonstrate enhanced bacteriolytic activity via improved cell wall targeting of autolysin catalytic domains.
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Affiliation(s)
- Daniel C Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth College, Hanover, NH, 03755, USA
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Salvat RS, Parker AS, Choi Y, Bailey-Kellogg C, Griswold KE. Mapping the Pareto optimal design space for a functionally deimmunized biotherapeutic candidate. PLoS Comput Biol 2015; 11:e1003988. [PMID: 25568954 PMCID: PMC4288714 DOI: 10.1371/journal.pcbi.1003988] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/14/2014] [Indexed: 12/25/2022] Open
Abstract
The immunogenicity of biotherapeutics can bottleneck development pipelines and poses a barrier to widespread clinical application. As a result, there is a growing need for improved deimmunization technologies. We have recently described algorithms that simultaneously optimize proteins for both reduced T cell epitope content and high-level function. In silico analysis of this dual objective design space reveals that there is no single global optimum with respect to protein deimmunization. Instead, mutagenic epitope deletion yields a spectrum of designs that exhibit tradeoffs between immunogenic potential and molecular function. The leading edge of this design space is the Pareto frontier, i.e. the undominated variants for which no other single design exhibits better performance in both criteria. Here, the Pareto frontier of a therapeutic enzyme has been designed, constructed, and evaluated experimentally. Various measures of protein performance were found to map a functional sequence space that correlated well with computational predictions. These results represent the first systematic and rigorous assessment of the functional penalty that must be paid for pursuing progressively more deimmunized biotherapeutic candidates. Given this capacity to rapidly assess and design for tradeoffs between protein immunogenicity and functionality, these algorithms may prove useful in augmenting, accelerating, and de-risking experimental deimmunization efforts. Protein therapeutics have created a revolution in disease therapy, providing improved outcomes for prevalent illnesses and conditions while at the same time yielding treatments for diseases that were previously intractable. However, this powerful class of drugs is subject to their own unique challenges and risk factors. In particular, the biological origins of therapeutic proteins predispose them towards eliciting a detrimental immune response from the patient's own body. Therefore, fully capitalizing on the medicinal reservoir of natural and engineered proteins will require efficient, effective, and broadly applicable deimmunization technologies. We have developed deimmunization algorithms that simultaneously optimize therapeutic candidates for both low immunogenicity and high-level activity and stability. Here, we combine computational modeling and experimental analysis to show that the process of protein deimmunization manifests inherent tradeoffs between immunogenic potential and biomolecular function. Our experimental results demonstrate that dual objective optimization allows us to assess and design for these tradeoffs, thereby enabling facile construction of deimmunized variants that span a broad range of immunogenicity and functionality performance parameters. Thus, we can rapidly map the design space for deimmunized drug candidates, and we can use this information to guide selection of engineered proteins that are most likely to meet performance benchmarks for a given clinical application.
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Affiliation(s)
- Regina S. Salvat
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America
| | - Andrew S. Parker
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
| | - Yoonjoo Choi
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
| | - Chris Bailey-Kellogg
- Department of Computer Science, Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail: (CBK); (KEG)
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth, Hanover, New Hampshire, United States of America
- Program in Molecular and Cellular Biology, Dartmouth, Hanover, New Hampshire, United States of America
- * E-mail: (CBK); (KEG)
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Baker I, Fiering SN, Griswold KE, Hoopes PJ, Kekalo K, Ndong C, Paulsen K, Petryk AA, Pogue B, Shubitidze F, Weaver J. The Dartmouth Center for Cancer Nanotechnology Excellence: magnetic hyperthermia. Nanomedicine (Lond) 2015; 10:1685-92. [PMID: 26080693 PMCID: PMC4493741 DOI: 10.2217/nnm.15.64] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Dartmouth Center for Cancer Nanotechnology Excellence - one of nine funded by the National Cancer Institute as part of the Alliance for Nanotechnology in Cancer - focuses on the use of magnetic nanoparticles for cancer diagnostics and hyperthermia therapy. It brings together a diverse team of engineers and biomedical researchers with expertise in nanomaterials, molecular targeting, advanced biomedical imaging and translational in vivo studies. The goal of successfully treating cancer is being approached by developing nanoparticles, conjugating them with Fabs, hyperthermia treatment, immunotherapy and sensing treatment response.
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Affiliation(s)
- Ian Baker
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Steve N Fiering
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - Karl E Griswold
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - P Jack Hoopes
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - Katerina Kekalo
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Christian Ndong
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
| | - Keith Paulsen
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Alicea A Petryk
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Brian Pogue
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - Fridon Shubitidze
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
| | - John Weaver
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH 03755, USA
- Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Lebanon, NH 03766, USA
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27
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Osipovitch DC, Griswold KE. Fusion with a cell wall binding domain renders autolysin LytM a potent anti-Staphylococcus aureus agent. FEMS Microbiol Lett 2014; 362:1-7. [PMID: 25670705 DOI: 10.1093/femsle/fnu035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [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: 02/07/2023] Open
Abstract
Despite intense efforts by the medical and pharmaceutical communities, Staphylococcus aureus continues to be a pervasive pathogen that causes a myriad of diseases and a high level of morbidity and mortality among infected patients. Thus, discovering or designing novel therapeutics able to kill both drug-resistant and drug-sensitive S. aureus remains a top priority. Bacteriolytic enzymes, mostly from phage, have shown great promise in preclinical studies, but little consideration has been given to cis-acting autolytic enzymes derived from the pathogen itself. Here, we use the S. aureus autolysin LytM as a proof of principal to demonstrate the antibacterial potential of endogenous peptidoglycan-degrading enzymes. While native LytM is only marginally bactericidal, fusion of LytM to the lysostaphin cell wall binding domain enhances its anti-staphylococcal activity approximately 540-fold, placing it on par with many phage lysins currently in preclinical development. The potential to therapeutically co-opt a pathogen's endogenous peptidoglycan recycling machinery opens the door to a previously untapped reservoir of antibacterial drug candidates.
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Affiliation(s)
- Daniel C Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth, Hanover, NH 03755, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH 03755, USA Program in Molecular and Cellular Biology, Dartmouth, Hanover, NH 03755, USA
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28
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Salvat R, Moise L, Bailey-Kellogg C, Griswold KE. A high throughput MHC II binding assay for quantitative analysis of peptide epitopes. J Vis Exp 2014. [PMID: 24686319 DOI: 10.3791/51308] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Biochemical assays with recombinant human MHC II molecules can provide rapid, quantitative insights into immunogenic epitope identification, deletion, or design(1,2). Here, a peptide-MHC II binding assay is scaled to 384-well format. The scaled down protocol reduces reagent costs by 75% and is higher throughput than previously described 96-well protocols(1,3-5). Specifically, the experimental design permits robust and reproducible analysis of up to 15 peptides against one MHC II allele per 384-well ELISA plate. Using a single liquid handling robot, this method allows one researcher to analyze approximately ninety test peptides in triplicate over a range of eight concentrations and four MHC II allele types in less than 48 hr. Others working in the fields of protein deimmunization or vaccine design and development may find the protocol to be useful in facilitating their own work. In particular, the step-by-step instructions and the visual format of JoVE should allow other users to quickly and easily establish this methodology in their own labs.
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Affiliation(s)
| | - Leonard Moise
- Institute for Immunology and Informatics, University of Rhode Island
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29
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Griswold KE, Bement JL, Teneback CC, Scanlon TC, Wargo MJ, Leclair LW. Bioengineered lysozyme in combination therapies for Pseudomonas aeruginosa lung infections. Bioengineered 2014; 5:143-7. [PMID: 24637705 DOI: 10.4161/bioe.28335] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 11/19/2022] Open
Abstract
There is increasing urgency in the battle against drug-resistant bacterial pathogens, and this public health crisis has created a desperate need for novel antimicrobial agents. Recombinant human lysozyme represents one interesting candidate for treating pulmonary infections, but the wild type enzyme is subject to electrostatic mediated inhibition by anionic biopolymers that accumulate in the infected lung. We have redesigned lysozyme's electrostatic potential field, creating a genetically engineered variant that is less susceptible to polyanion inhibition, yet retains potent bactericidal activity. A recent publication demonstrated that the engineered enzyme outperforms wild type lysozyme in a murine model of Pseudomonas aeruginosa lung infection. Here, we expand upon our initial studies and consider dual therapies that combine lysozymes with an antimicrobial peptide. Consistent with our earlier results, the charge modified lysozyme combination outperformed its wild type counterpart, yielding more than an order-of-magnitude reduction in bacterial burden following treatment with a single dose.
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Affiliation(s)
- Karl E Griswold
- Thayer School of Engineering; Dartmouth University; Hanover, NH USA; Department of Biological Sciences; Dartmouth University; Hanover, NH USA; Molecular and Cellular Biology Program; Dartmouth University; Hanover, NH USA
| | - Jenna L Bement
- University of Vermont College of Medicine; Division of Pulmonary and Critical Care Medicine; Burlington, VT USA
| | - Charlotte C Teneback
- University of Vermont College of Medicine; Division of Pulmonary and Critical Care Medicine; Burlington, VT USA
| | - Thomas C Scanlon
- Thayer School of Engineering; Dartmouth University; Hanover, NH USA
| | - Matthew J Wargo
- University of Vermont College of Medicine; Microbiology and Molecular Genetics; Burlington, VT USA
| | - Laurie W Leclair
- University of Vermont College of Medicine; Division of Pulmonary and Critical Care Medicine; Burlington, VT USA
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30
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Zhang X, Reeves DB, Perreard IM, Kett WC, Griswold KE, Gimi B, Weaver JB. Molecular sensing with magnetic nanoparticles using magnetic spectroscopy of nanoparticle Brownian motion. Biosens Bioelectron 2013; 50:441-6. [PMID: 23896525 PMCID: PMC3844855 DOI: 10.1016/j.bios.2013.06.049] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/20/2013] [Accepted: 06/24/2013] [Indexed: 01/02/2023]
Abstract
Functionalized magnetic nanoparticles (mNPs) have shown promise in biosensing and other biomedical applications. Here we use functionalized mNPs to develop a highly sensitive, versatile sensing strategy required in practical biological assays and potentially in vivo analysis. We demonstrate a new sensing scheme based on magnetic spectroscopy of nanoparticle Brownian motion (MSB) to quantitatively detect molecular targets. MSB uses the harmonics of oscillating mNPs as a metric for the freedom of rotational motion, thus reflecting the bound state of the mNP. The harmonics can be detected in vivo from nanogram quantities of iron within 5s. Using a streptavidin-biotin binding system, we show that the detection limit of the current MSB technique is lower than 150 pM (0.075 pmole), which is much more sensitive than previously reported techniques based on mNP detection. Using mNPs conjugated with two anti-thrombin DNA aptamers, we show that thrombin can be detected with high sensitivity (4 nM or 2 pmole). A DNA-DNA interaction was also investigated. The results demonstrated that sequence selective DNA detection can be achieved with 100 pM (0.05 pmole) sensitivity. The results of using MSB to sense these interactions, show that the MSB based sensing technique can achieve rapid measurement (within 10s), and is suitable for detecting and quantifying a wide range of biomarkers or analytes. It has the potential to be applied in variety of biomedical applications or diagnostic analyses.
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Affiliation(s)
- Xiaojuan Zhang
- Department of Radiology, Geisel School of Medicine, Dartmouth College, 1 Rope Ferry Road. Hanover, NH 03755-1404, United States
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31
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Scanlon TC, Dostal SM, Griswold KE. A high-throughput screen for antibiotic drug discovery. Biotechnol Bioeng 2013; 111:232-43. [PMID: 23955804 DOI: 10.1002/bit.25019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [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: 05/14/2013] [Revised: 07/21/2013] [Accepted: 07/29/2013] [Indexed: 11/10/2022]
Abstract
We describe an ultra-high-throughput screening platform enabling discovery and/or engineering of natural product antibiotics. The methodology involves creation of hydrogel-in-oil emulsions in which recombinant microorganisms are co-emulsified with bacterial pathogens; antibiotic activity is assayed by use of a fluorescent viability dye. We have successfully utilized both bulk emulsification and microfluidic technology for the generation of hydrogel microdroplets that are size-compatible with conventional flow cytometry. Hydrogel droplets are ∼25 pL in volume, and can be synthesized and sorted at rates exceeding 3,000 drops/s. Using this technique, we have achieved screening throughputs exceeding 5 million clones/day. Proof-of-concept experiments demonstrate efficient selection of antibiotic-secreting yeast from a vast excess of negative controls. In addition, we have successfully used this technique to screen a metagenomic library for secreted antibiotics that kill the human pathogen Staphylococcus aureus. Our results establish the practical utility of the screening platform, and we anticipate that the accessible nature of our methods will enable others seeking to identify and engineer the next generation of antibacterial biomolecules.
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Affiliation(s)
- Thomas C Scanlon
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, 03755
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32
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Abstract
Therapeutic proteins continue to yield revolutionary new treatments for a growing spectrum of human disease, but the development of these powerful drugs requires solving a unique set of challenges. For instance, it is increasingly apparent that mitigating potential anti-therapeutic immune responses, driven by molecular recognition of a therapeutic protein's peptide fragments, may be best accomplished early in the drug development process. One may eliminate immunogenic peptide fragments by mutating the cognate amino acid sequences, but deimmunizing mutations are constrained by the need for a folded, stable, and functional protein structure. These two concerns may be competing, as the mutations that are best at reducing immunogenicity often involve amino acids that are substantially different physicochemically. We develop a novel approach, called EpiSweep, that simultaneously optimizes both concerns. Our algorithm identifies sets of mutations making such Pareto optimal trade-offs between structure and immunogenicity, embodied by a molecular mechanics energy function and a T-cell epitope predictor, respectively. EpiSweep integrates structure-based protein design, sequence-based protein deimmunization, and algorithms for finding the Pareto frontier of a design space. While structure-based protein design is NP-hard, we employ integer programming techniques that are efficient in practice. Furthermore, EpiSweep only invokes the optimizer once per identified Pareto optimal design. We show that EpiSweep designs of regions of the therapeutics erythropoietin and staphylokinase are predicted to outperform previous experimental efforts. We also demonstrate EpiSweep's capacity for deimmunization of the entire proteins, case analyses involving dozens of predicted epitopes, and tens of thousands of unique side-chain interactions. Ultimately, Epi-Sweep is a powerful protein design tool that guides the protein engineer toward the most promising immunotolerant biotherapeutic candidates.
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Affiliation(s)
- Andrew S Parker
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
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33
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Abstract
Abstract
Introduction: Bacterial cytosine deaminase (CD) mediates the de novo conversion of the non-toxic prodrug, 5-fluorocytosine (5-FC) to its cytotoxic form, 5-fluorouracil (5-FU). Enzyme localization at the tumor site reduces systemic toxicity while increasing local drug availability. The in situ cellular expression of enzymes provides greater stability and control of enzyme activity as compared to isolated enzymes, and their on-demand expression can be achieved through transcriptional factors activated by stimuli such as heat. Bacterial λ PR promoter in conjunction with the cI857 repressor gene imparts thermoselectivity to enzyme expression - cloned vectors containing CD gene under the transcriptional control of this expression system preferentially produce CD at elevated temperatures, providing a thermal switch to trigger enzyme synthesis. Such enzyme-prodrug therapy, when timed to perform as an adjuvant to other treatment modalities such as magnetic nanoparticle hyperthermia, has the potential to enhance therapeutic index as a combination therapy.
Methods: CD gene was PCR amplified from pbCD540FT vector and cloned into pLDR20 vector. The CD gene was placed under the transcriptional control of λ PR promoter and cI857 thermosensitive repressor cassette. The cloned vector was transformed into NM522 competent cells. Positive colonies selected from LB-Agar-Ampicillin plates were cultured in LB-Ampicillin medium. CD gene was characterized by PCR amplification and cycle sequencing of the isolated plasmid DNA. Protein expression in cells grown at 30 °C and 42 °C was analyzed by SDS-PAGE followed by Coomassie blue staining. Enzyme activity in cells grown at 30 °C and 42 °C was compared by incubating engineered cells with 5-FC and spectrophotometrically measuring its conversion to 5-FU.
Results summary: The presence of CD gene in competent cells was verified by PCR amplification and cycle sequencing. We observed an enhanced expression of CD gene in the transformed cells at 42 °C as compared to 30 °C, from SDS-PAGE. Spectrophotometric analysis of enzyme activity showed an enhancement in cells grown at 42 °C. We are extending our work to combine enzyme-prodrug therapy with magnetic nanoparticle hyperthermia. We will coencapsulate our engineered cells with magnetic iron oxide nanoparticles (IONP) in immunoisolative sodium alginate microspheres. Localized heating during IONP hyperthermia can be a source of thermal stress for triggering enzyme expression resulting in the in situ synthesis of 5-FU. This combined therapy should enhance therapeutic index as compared to each of the therapies alone.
Acknowledgement: pbCD540FT was a kind gift from Prof. J. M. Brown, Stanford University School of Medicine. This work is supported by the Dartmouth Center of Cancer Nanotechnology Excellence pilot project grant, NIH U54 CA151662 (BG, NVK).
Citation Format: Venkata K. Nemani, Riley E. Ennis, Karl E. Griswold, Barjor Gimi. Heat-induced expression of cytosine deaminase for enzyme-prodrug therapy. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3300. doi:10.1158/1538-7445.AM2013-3300
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Affiliation(s)
- Venkata K. Nemani
- 1Department of Radiology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Riley E. Ennis
- 1Department of Radiology, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | | | - Barjor Gimi
- 1Department of Radiology, Geisel School of Medicine at Dartmouth, Lebanon, NH
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Choi Y, Griswold KE, Bailey-Kellogg C. Structure-based redesign of proteins for minimal T-cell epitope content. J Comput Chem 2013; 34:879-91. [PMID: 23299435 PMCID: PMC3763725 DOI: 10.1002/jcc.23213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Revised: 11/16/2012] [Accepted: 11/28/2012] [Indexed: 12/31/2022]
Abstract
The protein universe displays a wealth of therapeutically relevant activities, but T-cell driven immune responses to non-"self" biological agents present a major impediment to harnessing the full diversity of these molecular functions. Mutagenic T-cell epitope deletion seeks to mitigate the immune response, but can typically address only a small number of epitopes. Here, we pursue a "bottom-up" approach that redesigns an entire protein to remain native-like but contain few if any immunogenic epitopes. We do so by extending the Rosetta flexible-backbone protein design software with an epitope scoring mechanism and appropriate constraints. The method is benchmarked with a diverse panel of proteins and applied to three targets of therapeutic interest. We show that the deimmunized designs indeed have minimal predicted epitope content and are native-like in terms of various quality measures, and moreover that they display levels of native sequence recovery comparable to those of non-deimmunized designs.
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Affiliation(s)
- Yoonjoo Choi
- Department of Computer Science, Dartmouth College, New Hampshire 03755, USA
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Tate JA, Kett W, NDong C, Griswold KE, Hoopes PJ. Biodistribution of antibody-targeted and non-targeted iron oxide nanoparticles in a breast cancer mouse model. Proc SPIE Int Soc Opt Eng 2013; 8584:85840G. [PMID: 25301995 DOI: 10.1117/12.2008814] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Iron oxide nanoparticle (IONP) hyperthermia is a novel therapeutic strategy currently under consideration for the treatment of various cancer types. Systemic delivery of IONP followed by non-invasive activation via a local alternating magnetic field (AMF) results in site-specific energy deposition in the IONP-containing tumor. Targeting IONP to the tumor using an antibody or antibody fragment conjugated to the surface may enhance the intratumoral deposition of IONP and is currently being pursued by many nanoparticle researchers. This strategy, however, is subject to a variety of restrictions in the in vivo environment, where other aspects of IONP design will strongly influence the biodistribution. In these studies, various targeted IONP are compared to non-targeted controls. IONP were injected into BT-474 tumor-bearing NSG mice and tissues harvested 24hrs post-injection. Results indicate no significant difference between the various targeted IONP and the non-targeted controls, suggesting the IONP were prohibitively-sized to incur tumor penetration. Additional strategies are currently being pursued in conjuncture with targeted particles to increase the intratumoral deposition.
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Affiliation(s)
- Jennifer A Tate
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH, USA 03755-8000
| | - Warren Kett
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH, USA 03755-8000
| | - Christian NDong
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH, USA 03755-8000
| | - Karl E Griswold
- Thayer School of Engineering, 14 Engineering Drive, Hanover, NH, USA 03755-8000
| | - P Jack Hoopes
- Dartmouth Medical School, 1 Rope Ferry Road, Hanover, NH USA 03755-1404
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36
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Lamppa JW, Tanyos SA, Griswold KE. Engineering Escherichia coli for soluble expression and single step purification of active human lysozyme. J Biotechnol 2012; 164:1-8. [PMID: 23220215 DOI: 10.1016/j.jbiotec.2012.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 11/07/2012] [Accepted: 11/15/2012] [Indexed: 10/27/2022]
Abstract
Genetically engineered variants of human lysozyme represent promising leads in the battle against drug-resistant bacterial pathogens, but early stage development and testing of novel lysozyme variants is constrained by the lack of a robust, scalable and facile expression system. While wild type human lysozyme is reportedly produced at 50–80 kg per hectare of land in recombinant rice, this plant-based system is not readily scaled down to bench top production, and it is therefore not suitable for development and characterization of novel lysozyme variants. Here, we describe a novel and efficient expression system capable of producing folded, soluble and functional human lysozyme in Escherichia coli cells. To achieve this goal, we simultaneously co-express multiple protein folding chaperones as well as harness the lysozyme inhibitory protein, Ivy. Our strategy exploits E. coli's ease of culture, short doubling time, and facile genetics to yield upwards of 30 mg/l of soluble lysozyme in a bioreactor system, a 3000-fold improvement over prior efforts in E. coli. Additionally, molecular interactions between lysozyme and a his-tagged Ivy allows for one-step purification by IMAC, yielding as much as 21 mg/l of purified enzyme. We anticipate that our expression and purification platform will facilitate further development of engineered lysozymes having utility in disease treatment and other practical applications.
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Affiliation(s)
- John W Lamppa
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
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37
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Osipovitch DC, Parker AS, Makokha CD, Desrosiers J, Kett WC, Moise L, Bailey-Kellogg C, Griswold KE. Design and analysis of immune-evading enzymes for ADEPT therapy. Protein Eng Des Sel 2012; 25:613-23. [PMID: 22898588 DOI: 10.1093/protein/gzs044] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The unparalleled specificity and activity of therapeutic proteins has reshaped many aspects of modern clinical practice, and aggressive development of new protein drugs promises a continued revolution in disease therapy. As a result of their biological origins, however, therapeutic proteins present unique design challenges for the biomolecular engineer. For example, protein drugs are subject to immune surveillance within the patient's body; this anti-drug immune response can compromise therapeutic efficacy and even threaten patient safety. Thus, there is a growing demand for broadly applicable protein deimmunization strategies. We have recently developed optimization algorithms that integrate computational prediction of T-cell epitopes and bioinformatics-based assessment of the structural and functional consequences of epitope-deleting mutations. Here, we describe the first experimental validation of our deimmunization algorithms using Enterobacter cloacae P99 β-lactamase, a component of antibody-directed enzyme prodrug cancer therapies. Compared with wild-type or a previously deimmunized variant, our computationally optimized sequences exhibited significantly less in vitro binding to human type II major histocompatibility complex immune molecules. At the same time, our globally optimal design exhibited wild-type catalytic proficiency. We conclude that our deimmunization algorithms guide the protein engineer towards promising immunoevasive candidates and thereby have the potential to streamline biotherapeutic development.
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Affiliation(s)
- Daniel C Osipovitch
- Program in Experimental and Molecular Medicine, Geisel School of Medicine, Dartmouth, Hanover, NH 03784, USA
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38
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Abstract
Protein engineering by combinatorial site-directed mutagenesis evaluates a portion of the sequence space near a target protein, seeking variants with improved properties (e.g., stability, activity, immunogenicity). In order to improve the hit-rate of beneficial variants in such mutagenesis libraries, we develop methods to select optimal positions and corresponding sets of the mutations that will be used, in all combinations, in constructing a library for experimental evaluation. Our approach, OCoM (Optimization of Combinatorial Mutagenesis), encompasses both degenerate oligonucleotides and specified point mutations, and can be directed accordingly by requirements of experimental cost and library size. It evaluates the quality of the resulting library by one- and two-body sequence potentials, averaged over the variants. To ensure that it is not simply recapitulating extant sequences, it balances the quality of a library with an explicit evaluation of the novelty of its members. We show that, despite dealing with a combinatorial set of variants, in our approach the resulting library optimization problem is actually isomorphic to single-variant optimization. By the same token, this means that the two-body sequence potential results in an NP-hard optimization problem. We present an efficient dynamic programming algorithm for the one-body case and a practically-efficient integer programming approach for the general two-body case. We demonstrate the effectiveness of our approach in designing libraries for three different case study proteins targeted by previous combinatorial libraries--a green fluorescent protein, a cytochrome P450, and a beta lactamase. We found that OCoM worked quite efficiently in practice, requiring only 1 hour even for the massive design problem of selecting 18 mutations to generate 10⁷ variants of a 443-residue P450. We demonstrate the general ability of OCoM in enabling the protein engineer to explore and evaluate trade-offs between quality and novelty as well as library construction technique, and identify optimal libraries for experimental evaluation.
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Affiliation(s)
- Andrew S Parker
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
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Parker AS, Griswold KE, Bailey-Kellogg C. Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions. J Bioinform Comput Biol 2011; 9:207-29. [PMID: 21523929 DOI: 10.1142/s0219720011005471] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 02/28/2011] [Accepted: 03/01/2011] [Indexed: 11/18/2022]
Abstract
Exogenous enzymes, signaling peptides, and other classes of nonhuman proteins represent a potentially massive but largely untapped pool of biotherapeutic agents. Adapting a foreign protein for therapeutic use poses numerous design challenges. We focus here on one significant problem: modifying the protein to mitigate the immune response mounted against "non-self" proteins, while not adversely affecting the protein's stability or therapeutic activity. In order to propose such variants suitable for experimental evaluation, this paper develops a computational method to select sets of mutations predicted to delete immunogenic T-cell epitopes, as evaluated by a 9-mer potential, while simultaneously maintaining important residues and residue interactions, as evaluated by one- and two-body potentials. While this design problem is NP-hard, we develop an integer programming approach that works very well in practice. We demonstrate the effectiveness of our approach by developing plans for biotherapeutic proteins that, in previous studies, have been partially deimmunized via extensive experimental characterization and modification of limited segments. In contrast, our global optimization technique considers an entire protein and accounts for all residues, residue interactions, and epitopes in proposing candidates worth subjecting to experimental evaluation.
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Affiliation(s)
- Andrew S Parker
- Department of Computer Science, Dartmouth College, Sudikoff Laboratory, Hanover, NH 03755, USA.
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Gill A, Scanlon TC, Osipovitch DC, Madden DR, Griswold KE. Crystal structure of a charge engineered human lysozyme having enhanced bactericidal activity. PLoS One 2011; 6:e16788. [PMID: 21408218 PMCID: PMC3049763 DOI: 10.1371/journal.pone.0016788] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 01/14/2011] [Indexed: 11/18/2022] Open
Abstract
Human lysozyme is a key component of the innate immune system, and recombinant forms of the enzyme represent promising leads in the search for therapeutic agents able to treat drug-resistant infections. The wild type protein, however, fails to participate effectively in clearance of certain infections due to inherent functional limitations. For example, wild type lysozymes are subject to electrostatic sequestration and inactivation by anionic biopolymers in the infected airway. A charge engineered variant of human lysozyme has recently been shown to possess improved antibacterial activity in the presence of disease associated inhibitory molecules. Here, the 2.04 Å crystal structure of this variant is presented along with an analysis that provides molecular level insights into the origins of the protein's enhanced performance. The charge engineered variant's two mutated amino acids exhibit stabilizing interactions with adjacent native residues, and from a global perspective, the mutations cause no gross structural perturbations or loss of stability. Importantly, the two substitutions dramatically expand the negative electrostatic potential that, in the wild type enzyme, is restricted to a small region near the catalytic residues. The net result is a reduction in the overall strength of the engineered enzyme's electrostatic potential field, and it appears that the specific nature of this remodeled field underlies the variant's reduced susceptibility to inhibition by anionic biopolymers.
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Affiliation(s)
- Avinash Gill
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Thomas C. Scanlon
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Daniel C. Osipovitch
- Program in Experimental and Molecular Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Dean R. Madden
- Department of Biochemistry, Dartmouth Medical School, Dartmouth College, Hanover, New Hampshire, United States of America
- Program in Molecular and Cellular Biology, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
- Program in Molecular and Cellular Biology, Dartmouth College, Hanover, New Hampshire, United States of America
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
- * E-mail:
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Abstract
Most researchers confidently assume that transformation of recombinant plasmid libraries into microbial hosts followed by outgrowth of isolated colonies results in a "one cell-one mutant gene-one protein variant" paradigm. Indeed, this assumption is supported by the overwhelming majority of published studies employing bacterial expression hosts. In stark contrast, we recently reported on Saccharomyces cerevisiae libraries containing unexpectedly high frequencies of cells harboring heterogeneous mixtures of plasmids, so called Multiple Vector Transformants (MVT). Intriguingly, we observed that yeast MVT persist as a significant proportion of populations for multiple generations. MVT can lead to misidentification of isolated mutants loss of functionally enhanced clones, and unwitting propagation of false positives derived from contaminating control sequences. Such experimental complications can have devastating outcomes in the context of protein engineering by combinatorial library screening. Herein, we demonstrate that the phenomenon of MVT is not restricted to vectors bearing the CEN/ARSH origin of replication, but may be an even greater concern when using high copy 2 µm plasmids. To mitigate the risks associated with MVT, we have developed an optimized sequencing procedure that facilitates rapid and reliable identification of MVT among clones of interest. In our experience, MVT and their associated risks can be virtually eliminated by employing extended liquid outgrowths of transformed populations and archiving sequence-verified, monoclonal, mutant genes from cell-templated PCR amplicons.
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Affiliation(s)
- Thomas C Scanlon
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
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Lamppa JW, Ackerman ME, Lai JI, Scanlon TC, Griswold KE. Genetically engineered alginate lyase-PEG conjugates exhibit enhanced catalytic function and reduced immunoreactivity. PLoS One 2011; 6:e17042. [PMID: 21340021 PMCID: PMC3038863 DOI: 10.1371/journal.pone.0017042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 01/13/2011] [Indexed: 11/18/2022] Open
Abstract
Alginate lyase enzymes represent prospective biotherapeutic agents for treating bacterial infections, particularly in the cystic fibrosis airway. To effectively deimmunize one therapeutic candidate while maintaining high level catalytic proficiency, a combined genetic engineering-PEGylation strategy was implemented. Rationally designed, site-specific PEGylation variants were constructed by orthogonal maleimide-thiol coupling chemistry. In contrast to random PEGylation of the enzyme by NHS-ester mediated chemistry, controlled mono-PEGylation of A1-III alginate lyase produced a conjugate that maintained wild type levels of activity towards a model substrate. Significantly, the PEGylated variant exhibited enhanced solution phase kinetics with bacterial alginate, the ultimate therapeutic target. The immunoreactivity of the PEGylated enzyme was compared to a wild type control using in vitro binding studies with both enzyme-specific antibodies, from immunized New Zealand white rabbits, and a single chain antibody library, derived from a human volunteer. In both cases, the PEGylated enzyme was found to be substantially less immunoreactive. Underscoring the enzyme's potential for practical utility, >90% of adherent, mucoid, Pseudomonas aeruginosa biofilms were removed from abiotic surfaces following a one hour treatment with the PEGylated variant, whereas the wild type enzyme removed only 75% of biofilms in parallel studies. In aggregate, these results demonstrate that site-specific mono-PEGylation of genetically engineered A1-III alginate lyase yielded an enzyme with enhanced performance relative to therapeutically relevant metrics.
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Affiliation(s)
- John W. Lamppa
- Thayer School of Engineering, Dartmouth
College, Hanover, New Hampshire, United States of America
| | - Margaret E. Ackerman
- Thayer School of Engineering, Dartmouth
College, Hanover, New Hampshire, United States of America
| | - Jennifer I. Lai
- Department of Biological Engineering,
Massachusetts Institute of Technology, Boston, Massachusetts, United States of
America
| | - Thomas C. Scanlon
- Thayer School of Engineering, Dartmouth
College, Hanover, New Hampshire, United States of America
| | - Karl E. Griswold
- Thayer School of Engineering, Dartmouth
College, Hanover, New Hampshire, United States of America
- Department of Biological Sciences, Dartmouth
College, Hanover, New Hampshire, United States of America
- Program in Molecular and Cellular Biology,
Dartmouth College, Hanover, New Hampshire, United States of America
- * E-mail:
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Scanlon TC, Teneback CC, Gill A, Bement JL, Weiner JA, Lamppa JW, Leclair LW, Griswold KE. Enhanced antimicrobial activity of engineered human lysozyme. ACS Chem Biol 2010; 5:809-18. [PMID: 20604527 DOI: 10.1021/cb1001119] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [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
Lysozymes contain a disproportionately large fraction of cationic residues, and are thereby attracted toward the negatively charged surface of bacterial targets. Importantly, this conserved biophysical property may inhibit lysozyme antibacterial function during acute and chronic infections. A mouse model of acute pulmonary Pseudomonas aeruginosa infection demonstrated that anionic biopolymers accumulate to high concentrations in the infected lung, and the presence of these species correlates with decreased endogenous lysozyme activity. To develop antibacterial enzymes designed specifically to be used as antimicrobial agents in the infected airway, the electrostatic potential of human lysozyme (hLYS) was remodeled by protein engineering. A novel, high-throughput screen was implemented to functionally interrogate combinatorial libraries of charge-engineered hLYS proteins, and variants with improved bactericidal activity were isolated and characterized in detail. These studies illustrate a general mechanism by which polyanions inhibit lysozyme function, and they are the first direct demonstration that decreasing hLYS's net cationic character improves its antibacterial activity in the presence of disease-associated biopolymers. In addition to avoiding electrostatic sequestration, at least one charge-engineered variant also kills bacteria more rapidly in the absence of inhibitory biopolymers; this observation supports a novel hypothesis that tuning the cellular affinity of peptidoglycan hydrolases may be a general strategy for improving kinetics of bacterial killing.
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Affiliation(s)
| | - Charlotte C. Teneback
- The Vermont Lung Center, Department of Medicine, University of Vermont College of Medicine, Burlington, Vermont 05405
| | | | - Jenna L. Bement
- The Vermont Lung Center, Department of Medicine, University of Vermont College of Medicine, Burlington, Vermont 05405
| | | | | | - Laurie W. Leclair
- The Vermont Lung Center, Department of Medicine, University of Vermont College of Medicine, Burlington, Vermont 05405
| | - Karl E. Griswold
- Thayer School of Engineering
- Program in Molecular and Cellular Biology
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
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Zheng W, Griswold KE, Bailey-Kellogg C. Protein fragment swapping: a method for asymmetric, selective site-directed recombination. J Comput Biol 2010; 17:459-75. [PMID: 20377457 DOI: 10.1089/cmb.2009.0189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This article presents a new approach to site-directed recombination, swapping combinations of selected discontiguous fragments from a source protein in place of corresponding fragments of a target protein. By being both asymmetric (differentiating source and target) and selective (swapping discontiguous fragments), our method focuses experimental effort on a more restricted portion of sequence space, constructing hybrids that are more likely to have the properties that are the objective of the experiment. Furthermore, since the source and target need to be structurally homologous only locally (rather than overall), our method supports swapping fragments from functionally important regions of a source into a target "scaffold" (for example, to humanize an exogenous therapeutic protein). A protein fragment swapping plan is defined by the residue position boundaries of the fragments to be swapped; it is assessed by an average potential score over the resulting hybrid library, with singleton and pairwise terms evaluating the importance and fit of the swapped residues. While we prove that it is NP-hard to choose an optimal set of fragments under such a potential score, we develop an integer programming approach, which we call Swagmer, that works very well in practice. We demonstrate the effectiveness of our method in three swapping problems: selective recombination between beta-lactamases, activity swapping between glutathione transferases, and activity swapping between carboxylases and mutases in the purE family. We show that the selective recombination approach generates better plan (in terms of resulting potential score) than traditional site-directed recombination approaches. We also show that in all cases the optimized experiments are significantly better than ones that would result from stochastic methods.
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Affiliation(s)
- Wei Zheng
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755, USA
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Parker AS, Zheng W, Griswold KE, Bailey-Kellogg C. Optimization algorithms for functional deimmunization of therapeutic proteins. BMC Bioinformatics 2010; 11:180. [PMID: 20380721 PMCID: PMC2873530 DOI: 10.1186/1471-2105-11-180] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 04/09/2010] [Indexed: 11/10/2022] Open
Abstract
Background To develop protein therapeutics from exogenous sources, it is necessary to mitigate the risks of eliciting an anti-biotherapeutic immune response. A key aspect of the response is the recognition and surface display by antigen-presenting cells of epitopes, short peptide fragments derived from the foreign protein. Thus, developing minimal-epitope variants represents a powerful approach to deimmunizing protein therapeutics. Critically, mutations selected to reduce immunogenicity must not interfere with the protein's therapeutic activity. Results This paper develops methods to improve the likelihood of simultaneously reducing the anti-biotherapeutic immune response while maintaining therapeutic activity. A dynamic programming approach identifies optimal and near-optimal sets of conservative point mutations to minimize the occurrence of predicted T-cell epitopes in a target protein. In contrast with existing methods, those described here integrate analysis of immunogenicity and stability/activity, are broadly applicable to any protein class, guarantee global optimality, and provide sufficient flexibility for users to limit the total number of mutations and target MHC alleles of interest. The input is simply the primary amino acid sequence of the therapeutic candidate, although crystal structures and protein family sequence alignments may also be input when available. The output is a scored list of sets of point mutations predicted to reduce the protein's immunogenicity while maintaining structure and function. We demonstrate the effectiveness of our approach in a number of case study applications, showing that, in general, our best variants are predicted to be better than those produced by previous deimmunization efforts in terms of either immunogenicity or stability, or both factors. Conclusions By developing global optimization algorithms leveraging well-established immunogenicity and stability prediction techniques, we provide the protein engineer with a mechanism for exploring the favorable sequence space near a targeted protein therapeutic. Our mechanism not only helps identify designs more likely to be effective, but also provides insights into the interrelated implications of design choices.
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Affiliation(s)
- Andrew S Parker
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
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46
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Scanlon TC, Gray EC, Griswold KE. Quantifying and resolving multiple vector transformants in S. cerevisiae plasmid libraries. BMC Biotechnol 2009; 9:95. [PMID: 19930565 PMCID: PMC2784458 DOI: 10.1186/1472-6750-9-95] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 11/20/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In addition to providing the molecular machinery for transcription and translation, recombinant microbial expression hosts maintain the critical genotype-phenotype link that is essential for high throughput screening and recovery of proteins encoded by plasmid libraries. It is known that Escherichia coli cells can be simultaneously transformed with multiple unique plasmids and thusly complicate recombinant library screening experiments. As a result of their potential to yield misleading results, bacterial multiple vector transformants have been thoroughly characterized in previous model studies. In contrast to bacterial systems, there is little quantitative information available regarding multiple vector transformants in yeast. Saccharomyces cerevisiae is the most widely used eukaryotic platform for cell surface display, combinatorial protein engineering, and other recombinant library screens. In order to characterize the extent and nature of multiple vector transformants in this important host, plasmid-born gene libraries constructed by yeast homologous recombination were analyzed by DNA sequencing. RESULTS It was found that up to 90% of clones in yeast homologous recombination libraries may be multiple vector transformants, that on average these clones bear four or more unique mutant genes, and that these multiple vector cells persist as a significant proportion of library populations for greater than 24 hours during liquid outgrowth. Both vector concentration and vector to insert ratio influenced the library proportion of multiple vector transformants, but their population frequency was independent of transformation efficiency. Interestingly, the average number of plasmids born by multiple vector transformants did not vary with their library population proportion. CONCLUSION These results highlight the potential for multiple vector transformants to dominate yeast libraries constructed by homologous recombination. The previously unrecognized prevalence and persistence of multiply transformed yeast cells have important implications for yeast library screens. The quantitative information described herein should increase awareness of this issue, and the rapid sequencing approach developed for these studies should be widely useful for identifying multiple vector transformants and avoiding complications associated with cells that have acquired more than one unique plasmid.
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47
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Beagle JM, Apgar GA, Jones KL, Griswold KE, Radcliffe JS, Qiu X, Lightfoot DA, Iqbal MJ. The digestive fate of Escherichia coli glutamate dehydrogenase deoxyribonucleic acid from transgenic corn in diets fed to weanling pigs. J Anim Sci 2007; 84:597-607. [PMID: 16478951 DOI: 10.2527/2006.843597x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Corn containing genetically engineered plasmid DNA encoding an Escherichia coli glutamate dehydrogenase (gdhA) was fed to 19-d-old weanling swine to trace the digestive fate of the transgenic DNA. Eight pens of 8 pigs were fed a commercial (nongdhA) starter for 2 wk. One pig was randomly selected from each pen for 0-h control samples. The remaining 56 pigs were transitioned onto a corn-soybean meal diet and fed a diet containing 58% gdhA corn for approximately 1 wk; immediately thereafter, liver, 10th rib muscle, white blood cells, and plasma from the hepatic portal vein and ingesta from the stomach, distal ileum, and large intestine were collected. The DNA was extracted and the concentration determined via spectrophotometry. Polymerase chain reaction and gel electrophoresis were performed with primers designed to amplify 490 bp that included the plasmid's ligation site between the maize ubiquitin and the gdhA genes. The gdhA corn-derived DNA and diet served as positive assay controls, and conventional corn DNA and distilled water acted as negative assay controls. Detection limits were 0.99 fg of target DNA confounded with 500 ng of conventional corn DNA per each 20 &L reaction. Transgenic DNA was detected in 71.43% of the stomach and 1.79% of the ileal ingesta samples from treatment animals but was not detected in the large intestine, white blood cells, plasma, liver, or muscle samples. Transgenic DNA was not detected in any sample from 0-h control animals. Stomach and ileal ingesta samples were further analyzed using real-time PCR. With an estimated limit of detection of 1.049 ag/microL, 89.29% of the stomach ingesta samples were positive (average 1.56 fg target DNA). The proportion of transgenic DNA to total DNA differed between diet and stomach ingesta samples (P < 0.001). Despite the greater sensitivity of real-time PCR, target DNA was detected in only 1.79% of ileal ingesta. These data suggest that the gdhA transgene began degradation in the stomach and was nondetectable in the large intestine.
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Affiliation(s)
- J M Beagle
- Department of Animal Science, Food and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA
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Griswold KE, Aiyappan NS, Iverson BL, Georgiou G. The Evolution of Catalytic Efficiency and Substrate Promiscuity in Human Theta Class 1-1 Glutathione Transferase. J Mol Biol 2006; 364:400-10. [PMID: 17011574 PMCID: PMC1995603 DOI: 10.1016/j.jmb.2006.09.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [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] [Received: 07/21/2006] [Revised: 08/31/2006] [Accepted: 09/01/2006] [Indexed: 11/29/2022]
Abstract
Theta class glutathione transferases (GST) from various species exhibit markedly different catalytic activities in conjugating the tripeptide glutathione (GSH) to a variety of electrophilic substrates. For example, the human theta 1-1 enzyme (hGSTT1-1) is 440-fold less efficient than the rat theta 2-2 enzyme (rGSTT2-2) with the fluorogenic substrate 7-amino-4-chloromethyl coumarin (CMAC). Large libraries of hGSTT1-1 constructed by error-prone PCR, DNA shuffling, or saturation mutagenesis were screened for improved catalytic activity towards CMAC in a quantitative fashion using flow cytometry. An iterative directed evolution approach employing random mutagenesis in conjunction with homologous recombination gave rise to enzymes exhibiting up to a 20,000-fold increase in k(cat)/K(M) compared to hGSTT1-1. All highly active clones encoded one or more mutations at residues 32, 176, or 234. Combinatorial saturation mutagenesis was used to evaluate the full complement of natural amino acids at these positions, and resulted in the isolation of enzymes with catalytic rates comparable to those exhibited by the fastest mutants obtained via directed evolution. The substrate selectivities of enzymes resulting from random mutagenesis, DNA shuffling, and combinatorial saturation mutagenesis were evaluated using a series of distinct electrophiles. The results revealed that promiscuous substrate activities arose in a stochastic manner, as they did not correlate with catalytic efficiency towards the CMAC selection substrate. In contrast, chimeric enzymes previously constructed by homology-independent recombination of hGSTT-1 and rGSTT2-2 exhibited very different substrate promiscuity profiles, and showed a more defined relationship between evolved and promiscuous activities.
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Affiliation(s)
- Karl E. Griswold
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Nandini S. Aiyappan
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
| | - Brent L. Iverson
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- ‡ To whom correspondence should be addressed: , Department of Chemistry and Biochemistry, WEL 5.320, University of Texas at Austin, Austin, TX 78712, Phone 512-471-5053, Fax 512-471-8615, , Department of Chemical Engineering, CPE 4.410, University of Texas at Austin, Austin, TX 78712, Phone 512-471-6975, Fax 512-471-7963
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
- ‡ To whom correspondence should be addressed: , Department of Chemistry and Biochemistry, WEL 5.320, University of Texas at Austin, Austin, TX 78712, Phone 512-471-5053, Fax 512-471-8615, , Department of Chemical Engineering, CPE 4.410, University of Texas at Austin, Austin, TX 78712, Phone 512-471-6975, Fax 512-471-7963
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Callaway TR, Keen JE, Edrington TS, Baumgard LH, Spicer L, Fonda ES, Griswold KE, Overton TR, VanAmburgh ME, Anderson RC, Genovese KJ, Poole TL, Harvey RB, Nisbet DJ. Fecal prevalence and diversity of Salmonella species in lactating dairy cattle in four states. J Dairy Sci 2006; 88:3603-8. [PMID: 16162534 DOI: 10.3168/jds.s0022-0302(05)73045-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Salmonella is one of the most serious foodborne pathogenic bacteria in the United States, causing an estimated 1.3 million human illnesses each year. Dairy cows can be reservoirs of foodborne pathogenic bacteria, including Salmonella spp.; it is estimated that from 27 to 31% of dairy herds across the United States are colonized by Salmonella. The present study was designed to examine the occurrence of Salmonella spp. on dairies and to examine the serotypic diversity of Salmonella isolates on sampled dairies from across the United States. Fecal samples (n = 60 per dairy) were collected from 4 dairies in each of 4 states for a total of 960 fecal samples representing a total population of 13,200 dairy cattle. In the present study, 93 of 960 samples (9.96%) collected were culture-positive for Salmonella enterica. At least one Salmonella fecal-shedding cow was found in 9 of the 16 herds (56%) and the within-herd prevalence varied in our study from 0% in 7 herds to a maximum of 37% in 2 herds, with a mean prevalence among Salmonella-positive herds of 17%. Seventeen different serotypes were isolated, representing 7 different Salmonella serogroups. There were 2 or more different serogroups and serotypes present on 7 of the 9 Salmonella-positive farms. Serotypes Montevideo and Muenster were the most frequent and widespread. From our data, it appears that subclinical colonization with Salmonella enterica is relatively common on dairy farms and is represented by diverse serotypes on US dairy farms.
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Affiliation(s)
- T R Callaway
- Food and Feed Safety Research Unit, USDA/ARS, College Station, TX 77845, USA.
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50
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Abstract
We have used a compartmentalized in vitro selection method to directly select for ligase ribozymes that are capable of acting on and turning over separable oligonucleotide substrates. Starting from a degenerate pool, we selected a trans-acting variant of the Bartel class I ligase which statistically may have been the only active variant in the starting pool. The isolation of this sequence from the population suggests that this selection method is extremely robust at selecting optimal ribozymes and should, therefore, prove useful for the selection and optimization of other trans-acting nucleic acid catalysts capable of multiple turnover catalysis.
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Affiliation(s)
- Matthew Levy
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78751, USA
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