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Ma W, He C, Shen C, Zhang G, Pan J, Tang Y, Wang J, Gao T. Bead-based spontaneous Raman codes for multiplex immunoassay. Anal Chim Acta 2024; 1316:342813. [PMID: 38969419 DOI: 10.1016/j.aca.2024.342813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/29/2024] [Accepted: 06/01/2024] [Indexed: 07/07/2024]
Abstract
In the immunoassay process, for fulfilling the need to identify multiple analytes in a small amount of complex sample matrix, it is desirable to develop highly efficient and specific multiplex suspension array technology. Raman coding strategy offers an attractive solution to code the suspension arrays by simply combing narrow spectral bands with stable signal intensities through solid-phase synthesis on the resin beads. Based on this strategy, we report the bead-based spontaneous Raman codes for multiplex immunoassay. The study resulted in superior selectivity of the Raman-encoded beads for binding with single and multiple analytes, respectively. With the use of mixed types of Raman-encoded immunoassay beads, multiple targets in small amounts of samples were identified rapidly and accurately. By confirming the feasibility of bead-based spontaneous Raman codes for multiplex immunoassay, we anticipate this novel technology to be widely applied in the near future.
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Affiliation(s)
- Weiwei Ma
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Caili He
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Chengyue Shen
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Guihao Zhang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Jun Pan
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Yuchen Tang
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, China
| | - Jinzhi Wang
- Department of Chemistry, Shantou University Medical College, Shantou, 515041, Guangdong, China.
| | - Tingjuan Gao
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan, 430079, Hubei, China.
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2
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Hu X, Zhang M, Liu Y, Li YT, Li W, Li T, Li J, Xiao X, He Q, Zhang ZY, Zhang GJ. A portable transistor immunosensor for fast identification of porcine epidemic diarrhea virus. J Nanobiotechnology 2024; 22:239. [PMID: 38735951 PMCID: PMC11089749 DOI: 10.1186/s12951-024-02440-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 05/14/2024] Open
Abstract
Widespread distribution of porcine epidemic diarrhea virus (PEDV) has led to catastrophic losses to the global pig farming industry. As a result, there is an urgent need for rapid, sensitive and accurate tests for PEDV to enable timely and effective interventions. In the present study, we develop and validate a floating gate carbon nanotubes field-effect transistor (FG CNT-FET)-based portable immunosensor for rapid identification of PEDV in a sensitive and accurate manner. To improve the affinity, a unique PEDV spike protein-specific monoclonal antibody is prepared by purification, and subsequently modified on FG CNT-FET sensor to recognize PEDV. The developed FET biosensor enables highly sensitive detection (LoD: 8.1 fg/mL and 100.14 TCID50/mL for recombinant spike proteins and PEDV, respectively), as well as satisfactory specificity. Notably, an integrated portable platform consisting of a pluggable FG CNT-FET chip and a portable device can discriminate PEDV positive from negative samples and even identify PEDV and porcine deltacoronavirus within 1 min with 100% accuracy. The portable sensing platform offers the capability to quickly, sensitively and accurately identify PEDV, which further points to a possibility of point of care (POC) applications of large-scale surveillance in pig breeding facilities.
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Affiliation(s)
- Xiao Hu
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan, 430065, P.R. China
- Department of Pharmacy, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
| | - Mengjia Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Wuhan, 430070, P. R. China
| | - Yiwei Liu
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan, 411105, P. R. China
| | - Yu-Tao Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan, 430065, P.R. China
- Hubei Shizhen Laboratory, Wuhan, Hubei, 430065, P.R. China
| | - Wentao Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Wuhan, 430070, P. R. China
| | - Tingxian Li
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, P. R. China
| | - Jiahao Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan, 430065, P.R. China
| | - Xueqian Xiao
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan, 430065, P.R. China
| | - Qigai He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs, Wuhan, 430070, P. R. China.
| | - Zhi-Yong Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-based Electronics, School of Electronics, Peking University, Beijing, 100871, P. R. China.
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan, 430065, P.R. China.
- Hubei Shizhen Laboratory, Wuhan, Hubei, 430065, P.R. China.
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3
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Chen HM, Liu JX, Liu D, Hao GF, Yang GF. Human-virus protein-protein interactions maps assist in revealing the pathogenesis of viral infection. Rev Med Virol 2024; 34:e2517. [PMID: 38282401 DOI: 10.1002/rmv.2517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/12/2023] [Accepted: 01/16/2024] [Indexed: 01/30/2024]
Abstract
Many significant viral infections have been recorded in human history, which have caused enormous negative impacts worldwide. Human-virus protein-protein interactions (PPIs) mediate viral infection and immune processes in the host. The identification, quantification, localization, and construction of human-virus PPIs maps are critical prerequisites for understanding the biophysical basis of the viral invasion process and characterising the framework for all protein functions. With the technological revolution and the introduction of artificial intelligence, the human-virus PPIs maps have been expanded rapidly in the past decade and shed light on solving complicated biomedical problems. However, there is still a lack of prospective insight into the field. In this work, we comprehensively review and compare the effectiveness, potential, and limitations of diverse approaches for constructing large-scale PPIs maps in human-virus, including experimental methods based on biophysics and biochemistry, databases of human-virus PPIs, computational methods based on artificial intelligence, and tools for visualising PPIs maps. The work aims to provide a toolbox for researchers, hoping to better assist in deciphering the relationship between humans and viruses.
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Affiliation(s)
- Hui-Min Chen
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China
| | - Jia-Xin Liu
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan, China
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4
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Janezic EM, Doan A, Mai E, Bravo DD, Wang J, Kim HS, Spiess C, Bewley K, ElSohly A, Liang WC, Koerber JT, Richalet P, Vanhove M, Comps-Agrar L. A novel, label-free, pre-equilibrium assay to determine the association and dissociation rate constants of therapeutic antibodies on living cells. Br J Pharmacol 2023. [PMID: 37783572 DOI: 10.1111/bph.16258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/19/2023] [Accepted: 09/23/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND AND PURPOSE Monoclonal antibodies (Ab) represent the fastest growing drug class. Knowledge of the biophysical parameters (kon , koff and KD ) that dictate Ab:receptor interaction is critical during the drug discovery process. However, with the increasing complexity of Ab formats and their targets, it became apparent that existing technologies present limitations and are not always suitable to determine these parameters. Therefore, novel affinity determination methods represent an unmet assay need. EXPERIMENTAL APPROACH We developed a pre-equilibrium kinetic exclusion assay using recent mathematical advances to determine the kon , koff and KD of monoclonal Ab:receptor interactions on living cells. The assay is amenable to all human IgG1 and rabbit Abs. KEY RESULTS Using our novel assay, we demonstrated for several monoclonal Ab:receptor pairs that the calculated kinetic rate constants were comparable with orthogonal methods that were lower throughput or more resource consuming. We ran simulations to predict the critical conditions to improve the performance of the assays. We further showed that this method could successfully be applied to both suspension and adherent cells. Finally, we demonstrated that kon and koff , but not KD , correlate with in vitro potency for a panel of monoclonal Abs. CONCLUSIONS AND IMPLICATIONS Our novel assay has the potential to systematically probe binding kinetics of monoclonal Abs to cells and can be incorporated in a screening cascade to identify new therapeutic candidates. Wide-spread adoption of pre-equilibrium assays using physiologically relevant systems will lead to a more holistic understanding of how Ab binding kinetics influence their potency.
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Affiliation(s)
| | | | - Elaine Mai
- Genentech, Inc, South San Francisco, California, USA
| | | | - Jianyong Wang
- Genentech, Inc, South San Francisco, California, USA
| | - Hok Seon Kim
- Genentech, Inc, South San Francisco, California, USA
| | | | | | - Adel ElSohly
- Genentech, Inc, South San Francisco, California, USA
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5
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Crowley AR, Mehlenbacher MR, Sajadi MM, DeVico AL, Lewis GK, Ackerman ME. Evidence of variable human Fcγ receptor-Fc affinities across differentially-complexed IgG. MAbs 2023; 15:2231128. [PMID: 37405954 PMCID: PMC10324447 DOI: 10.1080/19420862.2023.2231128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023] Open
Abstract
Antibody-mediated effector functions are widely considered to unfold according to an associative model of IgG-Fcγ receptor (FcγR) interactions. The associative model presupposes that Fc receptors cannot discriminate antigen-bound IgG from free IgG in solution and have equivalent affinities for each. Therefore, the clustering of Fcγ receptors (FcγR) in the cell membrane, cross-activation of intracellular signaling domains, and the formation of the immune synapse are all the result of avid interactions between the Fc region of IgG and FcγRs that collectively overcome the individually weak, transient interactions between binding partners. Antibody allostery, specifically conformational allostery, is a competing model in which antigen-bound antibody molecules undergo a physical rearrangement that causes them to stand out from the background of free IgG by virtue of greater FcγR affinity. Various evidence exists in support of this model of antibody allostery, but it remains controversial. We report observations from multiplexed, label-free kinetic experiments in which the affinity values of FcγR were characterized for covalently immobilized, captured, and antigen-bound IgG. Across the strategies tested, receptors had greater affinity for the antigen-bound mode of IgG presentation. This phenomenon was observed across multiple FcγRs and generalized to multiple antigens, antibody specificities, and subclasses. Furthermore, the thermodynamic signatures of FcγR binding to free or immune-complexed IgG in solution differed when measured by an orthogonal label-free method, but the failure to recapitulate the trend in overall affinity leaves open questions as to what additional factors may be at play.
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Affiliation(s)
- Andrew R. Crowley
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
| | | | - Mohammad M. Sajadi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
- Baltimore VA Medical Center, VA Maryland Health Care System, Baltimore, USA
| | - Anthony L. DeVico
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - George K. Lewis
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
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6
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Joyce A, Shea C, You Z, Gorovits B, Lepsy C. Determination of Anti-drug Antibody Affinity in Clinical Study Samples Provides a Tool for Evaluation of Immune Response Maturation. AAPS J 2022; 24:114. [PMID: 36324032 PMCID: PMC9629885 DOI: 10.1208/s12248-022-00759-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Characterization of clinical anti-drug antibody (ADA) responses to biotherapeutics can be important to understanding the consequences of immunogenicity. ADA are expected to be polyclonal, with composition and affinities that evolve over time. Measuring ADA binding affinity can be complicated by the polyclonal nature of response, residual drug in sample, and low ADA levels. We developed a novel workflow to determine the apparent ADA affinity (KD) against a monoclonal antibody biotherapeutic, PF-06480605. An affinity capture elution pre-treatment step was used to isolate ADA and remove residual drug interference from samples. Solution-phase equilibrium incubation was performed using drug and sample ADA as variable and fixed binding interactants, respectively. Unbound ADA concentration was measured using a Singulex Erenna ligand-binding assay (LBA) method. Apparent ADA KD values were calculated using a custom R Shiny algorithm. KD values determined for ADA positive samples showed good correlation with other immunogenicity parameters, including titers and neutralizing antibody (NAb) activity with a general increase in affinity over time, indicative of a maturing immune response. Time of onset of high affinity responses (KD < 100 pM) varied between patients, ranging from 16 to 24 weeks. Antibody responses appeared monophasic at earlier time points, trending towards a biphasic response with a variable transition time and general increase in proportion of high affinity ADA over time. Herein, we provide a novel, sensitive bioanalytical method to determine the KD of ADA in clinical samples. The observed decrease in ADA KD is consistent with evidence of a maturing immune response.
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Affiliation(s)
- Alison Joyce
- grid.410513.20000 0000 8800 7493Pfizer, Inc., Worldwide Research & Development, Biomedicine Design, 1 Burtt Road, Andover, Massachusetts USA
| | - Christopher Shea
- grid.410513.20000 0000 8800 7493Pfizer, Inc., Worldwide Research & Development, Biomedicine Design, 1 Burtt Road, Andover, Massachusetts USA
| | - Zhiping You
- grid.410513.20000 0000 8800 7493Pfizer, Inc, Worldwide Research & Development, Early Clinical Development, 1 Burtt Road, Andover, Massachusetts USA
| | - Boris Gorovits
- grid.410513.20000 0000 8800 7493Pfizer, Inc., Worldwide Research & Development, Biomedicine Design, 1 Burtt Road, Andover, Massachusetts USA ,grid.510014.1Present Address: Development Sciences, Sana Biotechnology, Inc., 300 Technology Square, Cambridge, Massachusetts USA
| | - Christopher Lepsy
- grid.410513.20000 0000 8800 7493Pfizer, Inc., Worldwide Research & Development, Biomedicine Design, 1 Burtt Road, Andover, Massachusetts USA
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7
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Krieg D, Winter G, Svilenov HL. It is never too late for a cocktail - Development and analytical characterization of fixed-dose antibody combinations. J Pharm Sci 2022; 111:2149-2157. [DOI: 10.1016/j.xphs.2022.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022]
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8
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Kamat V, Boutot C, Rafique A, Granados C, Wang J, Badithe A, Torres M, Chatterjee I, Olsen O, Olson W, Huang T. High affinity human Fc specific monoclonal antibodies for capture kinetic analyses of antibody-antigen interactions. Anal Biochem 2022; 640:114455. [PMID: 34788604 DOI: 10.1016/j.ab.2021.114455] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022]
Abstract
We recently demonstrated that capturing human monoclonal antibodies (hmAbs) using high affinity anti-human Fc (AHC) antibodies allows reliable characterization of antibody-antigen interactions. Here, we characterized six human Fc specific mouse monoclonal antibodies (mAbs) and compared their binding profiles with three previously characterized goat AHC polyclonal antibodies (pAbs), exhibiting properties of a good capture reagent. All six mouse AHC mAbs specifically bound with high affinity to the Fc region of hIgG1, hIgG2, hIgG4 and to 43 different hIgG variants, containing substitutions and/or mutations in the hinge and/or Fc region, that have been reported to exhibit modified antibody effector function and/or pharmacokinetics. Biacore sensor surfaces individually derivatized with mouse AHC mAbs exhibited >2.5-fold higher hIgG binding capacity compared to the three goat AHC pAb surfaces and reproducibly captured hIgG over 300 capture-regeneration cycles. The results of the capture kinetic analyses performed on 31 antibody-antigen interactions using surfaces derivatized with either of the two highest affinity AHC mAbs (REGN7942 or REGN7943) were in concordance with those performed using goat AHC pAb surfaces. Our data demonstrate that AHC mAbs such as REGN7942 and REGN7943 that have properties superior than the three goat AHC pAbs are highly valuable research reagents, especially to perform capture kinetic analyses of antibody-antigen interactions on optical biosensors.
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Affiliation(s)
- Vishal Kamat
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA.
| | | | | | | | - Jing Wang
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
| | - Ashok Badithe
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
| | | | | | - Olav Olsen
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
| | - William Olson
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
| | - Tammy Huang
- Therapeutic Proteins, Regeneron Pharmaceuticals, USA
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9
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Almughamsi HM, Howell KM, Parry SR, Esene JE, Nielsen JB, Nordin GP, Woolley AT. Immunoaffinity monoliths for multiplexed extraction of preterm birth biomarkers from human blood serum in 3D printed microfluidic devices. Analyst 2022; 147:734-743. [PMID: 35103723 PMCID: PMC8849610 DOI: 10.1039/d1an01365c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In an effort to develop biomarker-based diagnostics for preterm birth (PTB) risk, we created 3D printed microfluidic devices with multiplexed immunoaffinity monoliths to selectively extract multiple PTB biomarkers. The equilibrium dissociation constant for each monoclonal antibody toward its target PTB biomarker was determined. We confirmed the covalent attachment of three different individual antibodies to affinity monoliths using fluorescence imaging. Three different PTB biomarkers were successfully extracted from human blood serum using their respective single-antibody columns. Selective binding of each antibody toward its target biomarker was observed. Finally, we extracted and eluted three PTB biomarkers from depleted human blood serum in multiplexed immunoaffinity columns in 3D printed microfluidic devices. This is the first demonstration of multiplexed immunoaffinity extraction of PTB biomarkers in 3D printed microfluidic devices.
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Affiliation(s)
- Haifa M. Almughamsi
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Karyna M. Howell
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Samuel R. Parry
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Joule E. Esene
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Jacob B. Nielsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Gregory P. Nordin
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT, 84602, USA
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA,corresponding author: ; 1-801-422-1701
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10
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Ji L, Waduge P, Hao L, Kaur A, Wan W, Wu Y, Tian H, Zhang J, Webster KA, Li W. Selectively targeting disease-restricted secretogranin III to alleviate choroidal neovascularization. FASEB J 2022; 36:e22106. [PMID: 34918375 PMCID: PMC8694659 DOI: 10.1096/fj.202101085rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 01/03/2023]
Abstract
Choroidal neovascularization (CNV), a leading cause of blindness in the elderly, is routinely treated with vascular endothelial growth factor (VEGF) inhibitors that have limited efficacy and potentially adverse side effects. An unmet clinical need is to develop novel therapies against other angiogenic factors for alternative or combination treatment to improve efficacy and safety. We recently described secretogranin III (Scg3) as a disease-selective angiogenic factor, causally linked to diabetic retinopathy and acting independently of the VEGF pathway. An important question is whether such a disease-selective Scg3 pathway contributes to other states of pathological angiogenesis beyond diabetic retinopathy. By applying a novel in vivo endothelial ligand binding assay, we found that the binding of Scg3 to CNV vessels in live mice was markedly increased over background binding to healthy choriocapillaris and blocked by an Scg3-neutralizing antibody, whereas VEGF showed no such differential binding. Intravitreal injection of anti-Scg3 humanized antibody Fab (hFab) inhibited Matrigel-induced CNV with similar efficacy to the anti-VEGF drug aflibercept. Importantly, a combination of anti-Scg3 hFab and aflibercept synergistically alleviated CNV. Homozygous deletion of the Scg3 gene markedly reduced CNV severity and abolished the therapeutic activity of anti-Scg3 hFab, but not aflibercept, suggesting a role for Scg3 in VEGF-independent CNV pathogenesis and therapy. Our work demonstrates the stringent disease selectivity of Scg3 binding and positions anti-Scg3 hFab as a next-generation disease-targeted anti-angiogenic therapy for CNV.
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Affiliation(s)
- Liyang Ji
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, TX.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL.,Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Prabuddha Waduge
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, TX.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL
| | - Lili Hao
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL.,Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Avinash Kaur
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, TX.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL
| | - Wencui Wan
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL.,Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Wu
- Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL
| | - Hong Tian
- Everglades Biopharma, LLC, Houston, TX
| | - Jinsong Zhang
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Keith A. Webster
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, TX.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL.,Everglades Biopharma, LLC, Houston, TX
| | - Wei Li
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, TX.,Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL
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11
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Duan Y, Chen R, Huang Y, Meng X, Chen J, Liao C, Tang Y, Zhou C, Gao X, Sun J. Tuning the ignition of CAR: optimizing the affinity of scFv to improve CAR-T therapy. Cell Mol Life Sci 2021; 79:14. [PMID: 34966954 PMCID: PMC11073403 DOI: 10.1007/s00018-021-04089-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 10/19/2022]
Abstract
How single-chain variable fragments (scFvs) affect the functions of chimeric antigen receptors (CARs) has not been well studied. Here, the components of CAR with an emphasis on scFv were described, and then several methods to measure scFv affinity were discussed. Next, scFv optimization studies for CD19, CD38, HER2, GD2 or EGFR were overviewed, showing that tuning the affinity of scFv could alleviate the on-target/off-tumor toxicity. The affinities of scFvs for different antigens were also summarized to designate a relatively optimal working range for CAR design. Last, a synthetic biology approach utilizing a low-affinity synthetic Notch (synNotch) receptor to achieve ultrasensitivity of antigen-density discrimination and murine models to assay the on-target/off-tumor toxicity of CARs were highlighted. Thus, this review provides preliminary guidelines of choosing the right scFvs for CARs.
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Affiliation(s)
- Yanting Duan
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Ruoqi Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Yanjie Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Xianhui Meng
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Jiangqing Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, Zhejiang, China
| | - Chan Liao
- Department of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yongmin Tang
- Department of Hematology-Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chun Zhou
- School of Public Health, and Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaofei Gao
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jie Sun
- Bone Marrow Transplantation Center of the First Affiliated Hospital & Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
- Institute of Hematology, Zhejiang University & Zhejiang Engineering Laboratory for Stem Cell and Immunotherapy, Hangzhou, Zhejiang, China.
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12
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Dash R, Singh SK, Chirmule N, Rathore AS. Assessment of Functional Characterization and Comparability of Biotherapeutics: a Review. AAPS J 2021; 24:15. [PMID: 34931298 DOI: 10.1208/s12248-021-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/30/2021] [Indexed: 11/30/2022] Open
Abstract
The development of monoclonal antibody (mAb) biosimilars is a complex process. The key to their successful development and commercialization is an in-depth understanding of the key product attributes that impact safety and efficacy and the strategies to control them. Functional assessment of mAb is a crucial part of the comparability of biopharmaceutical drugs. The development of a relevant and robust functional assay requires an interdisciplinary approach and sufficient flexibility to balance regulatory concerns as well as dynamics and variability during the manufacturing process. Although many advanced tools are available to study and compare the potency and bioactivity of the protein, most of these techniques suffer from major shortcomings that limit their routine use. These include the complexity of the task, establishment of the relevance of the chosen method with the mechanism of action (MOA) of the biosimilar, cost and extended time of analysis, and often the ambiguity in interpretation of the resulting data. To overcome or to address these challenges, the use of multiple orthogonal state-of-the-art techniques is a necessary prerequisite.
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Affiliation(s)
- Rozaleen Dash
- Department of Chemical Engineering, DBT Center of Excellence for Biopharmaceutical Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Sumit Kumar Singh
- Department of Chemical Engineering, DBT Center of Excellence for Biopharmaceutical Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.,School of Biochemical Engineering, IIT-BHU, Varanasi, India
| | | | - Anurag S Rathore
- Department of Chemical Engineering, DBT Center of Excellence for Biopharmaceutical Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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13
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Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Herlands L, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape. eLife 2021; 10:73027. [PMID: 34874007 PMCID: PMC8651292 DOI: 10.7554/elife.73027] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/07/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of SARS-CoV-2 variants threatens current vaccines and therapeutic antibodies and urgently demands powerful new therapeutics that can resist viral escape. We therefore generated a large nanobody repertoire to saturate the distinct and highly conserved available epitope space of SARS-CoV-2 spike, including the S1 receptor binding domain, N-terminal domain, and the S2 subunit, to identify new nanobody binding sites that may reflect novel mechanisms of viral neutralization. Structural mapping and functional assays show that indeed these highly stable monovalent nanobodies potently inhibit SARS-CoV-2 infection, display numerous neutralization mechanisms, are effective against emerging variants of concern, and are resistant to mutational escape. Rational combinations of these nanobodies that bind to distinct sites within and between spike subunits exhibit extraordinary synergy and suggest multiple tailored therapeutic and prophylactic strategies.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States.,Department of Chemistry, St. John's University, Queens, United States
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Magdalena Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States
| | - Nicholas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, United States
| | - Jacob B Jiler
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | | | | | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States.,Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, United States
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States.,Department of Biochemistry, University of Washington, Seattle, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
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14
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Spatola BN, Lerner AG, Wong C, Dela Cruz T, Welch M, Fung W, Kovalenko M, Losenkova K, Yegutkin GG, Beers C, Corbin J, Soros VB. Fully human anti-CD39 antibody potently inhibits ATPase activity in cancer cells via uncompetitive allosteric mechanism. MAbs 2021; 12:1838036. [PMID: 33146056 PMCID: PMC7646477 DOI: 10.1080/19420862.2020.1838036] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The extracellular ATP/adenosine axis in the tumor microenvironment (TME) has emerged as an important immune-regulatory pathway. Nucleoside triphosphate diphosphohydrolase-1 (NTPDase1), otherwise known as CD39, is highly expressed in the TME, both on infiltrating immune cells and tumor cells across a broad set of cancer indications. CD39 processes pro-inflammatory extracellular ATP to ADP and AMP, which is then processed by Ecto-5ʹ-nucleotidase/CD73 to immunosuppressive adenosine. Directly inhibiting the enzymatic function of CD39 via an antibody has the potential to unleash an immune-mediated anti-tumor response via two mechanisms: 1) increasing the availability of immunostimulatory extracellular ATP released by damaged and/or dying cells, and 2) reducing the generation and accumulation of suppressive adenosine within the TME. Tizona Therapeutics has engineered a novel first-in-class fully human anti-CD39 antibody, TTX-030, that directly inhibits CD39 ATPase enzymatic function with sub-nanomolar potency. Further characterization of the mechanism of inhibition by TTX-030 using CD39+ human melanoma cell line SK-MEL-28 revealed an uncompetitive allosteric mechanism (α < 1). The uncompetitive mechanism of action enables TTX-030 to inhibit CD39 at the elevated ATP concentrations reported in the TME. Maximal inhibition of cellular CD39 ATPase velocity was 85%, which compares favorably to results reported for antibody inhibitors to other enzyme targets. The allosteric mechanism of TTX-030 was confirmed via mapping the epitope to a region of CD39 distant from its active site, which suggests possible models for how potent inhibition is achieved. In summary, TTX-030 is a potent allosteric inhibitor of CD39 ATPase activity that is currently being evaluated in clinical trials for cancer therapy.
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Affiliation(s)
- Bradley N Spatola
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
| | - Alana G Lerner
- Immunology, Tizona Therapeutics , South San Francisco, CA, USA
| | - Clifford Wong
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
| | - Tracy Dela Cruz
- Immunology, Tizona Therapeutics , South San Francisco, CA, USA.,Immunology, Trishula Therapeutics, South San Francisco , CA, USA
| | - Megan Welch
- Immunology, Tizona Therapeutics , South San Francisco, CA, USA
| | - Wanchi Fung
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
| | | | | | | | - Courtney Beers
- Immunology, Tizona Therapeutics , South San Francisco, CA, USA
| | - John Corbin
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
| | - Vanessa B Soros
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
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15
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Tahir S, Bourquard T, Musnier A, Jullian Y, Corde Y, Omahdi Z, Mathias L, Reiter E, Crépieux P, Bruneau G, Poupon A. Accurate determination of epitope for antibodies with unknown 3D structures. MAbs 2021; 13:1961349. [PMID: 34432559 PMCID: PMC8405158 DOI: 10.1080/19420862.2021.1961349] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
MAbTope is a docking-based method for the determination of epitopes. It has been used to successfully determine the epitopes of antibodies with known 3D structures. However, during the antibody discovery process, this structural information is rarely available. Although we already have evidence that homology models of antibodies could be used instead of their 3D structure, the choice of the template, the methodology for homology modeling and the resulting performance still have to be clarified. Here, we show that MAbTope has the same performance when working with homology models of the antibodies as compared to crystallographic structures. Moreover, we show that even low-quality models can be used. We applied MAbTope to determine the epitope of dupilumab, an anti- interleukin 4 receptor alpha subunit therapeutic antibody of unknown 3D structure, that we validated experimentally. Finally, we show how the MAbTope-determined epitopes for a series of antibodies targeting the same protein can be used to predict competitions, and demonstrate the accuracy with an experimentally validated example. 3D: three-dimensionalRMSD: root mean square deviationCDR: complementary-determining regionCPU: central processing unitsVH: heavy chain variable regionVL: light chain variable regionscFv: single-chain variable fragmentsVHH: single-chain antibody variable regionIL4Rα: Interleukin 4 receptor alpha chainSPR: surface plasmon resonancePDB: protein data bankHEK293: Human embryonic kidney 293 cellsEDTA: Ethylenediaminetetraacetic acidFBS: Fetal bovine serumANOVA: Analysis of varianceEGFR: Epidermal growth factor receptorPE: PhycoerythrinAPC: AllophycocyaninFSC: forward scatterSSC: side scatterWT: wild type Keywords: MAbTope, Epitope Mapping, Molecular docking, Antibody modeling, Antibody-antigen docking
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Affiliation(s)
- Shifa Tahir
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France
| | - Thomas Bourquard
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,MAbSilico SAS, 1 Impasse Du Palais
| | - Astrid Musnier
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,MAbSilico SAS, 1 Impasse Du Palais
| | - Yann Jullian
- MAbSilico SAS, 1 Impasse Du Palais.,CaSciModOT, UFR De Sciences Et Techniques, Université De Tours
| | | | | | | | - Eric Reiter
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,France Inria, Inria Saclay-Île-de-France, Palaiseau, France.,Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Pascale Crépieux
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,France Inria, Inria Saclay-Île-de-France, Palaiseau, France.,Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | | | - Anne Poupon
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,MAbSilico SAS, 1 Impasse Du Palais.,France Inria, Inria Saclay-Île-de-France, Palaiseau, France.,Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
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16
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Budroni S, Buricchi F, Cavallone A, Volpini G, Mariani A, Lo Surdo P, Blohmke CJ, Del Giudice G, Medini D, Finco O. Computational modeling of microfluidic data provides high-throughput affinity estimates for monoclonal antibodies. Comput Struct Biotechnol J 2021; 19:3664-3672. [PMID: 34257845 PMCID: PMC8255181 DOI: 10.1016/j.csbj.2021.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 10/27/2022] Open
Abstract
Affinity measurement is a fundamental step in the discovery of monoclonal antibodies (mAbs) and of antigens suitable for vaccine development. Innovative affinity assays are needed due to the low throughput and/or limited dynamic range of available technologies. We combined microfluidic technology with quantum-mechanical scattering theory, in order to develop a high-throughput, broad-range methodology to measure affinity. Fluorescence intensity profiles were generated for out-of-equilibrium solutions of labelled mAbs and their antigen-binding fragments migrating along micro-columns with immobilized cognate antigen. Affinity quantification was performed by computational data analysis based on the Landau probability distribution. Experiments using a wide array of human or murine antibodies against bacterial or viral, protein or polysaccharide antigens, showed that all the antibody-antigen capture profiles (n = 841) generated at different concentrations were accurately described by the Landau distribution. A scale parameter W, proportional to the full-width-at-half-maximum of the capture profile, was shown to be independent of the antibody concentration. The W parameter correlated significantly (Pearson's r [p-value]: 0.89 [3 × 10-8]) with the equilibrium dissociation constant KD, a gold-standard affinity measure. Our method showed good intermediate precision (median coefficient of variation: 5%) and a dynamic range corresponding to KD values spanning from ~10-7 to ~10-11 Molar. Relative to assays relying on antibody-antigen equilibrium in solution, even when they are microfluidic-based, the method's turnaround times were decreased from 2 days to 2 h. The described computational modelling of antibody capture profiles represents a fast, reproducible, high-throughput methodology to accurately measure a broad range of antibody affinities in very low volumes of solution.
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17
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Qiao SP, Liu ZN, Li HC, He X, Pan H, Gao YZ. Construction of a CRISPR-Biolayer Interferometry Platform for Real-Time, Sensitive, and Specific DNA Detection. Chembiochem 2021; 22:1974-1984. [PMID: 33682991 DOI: 10.1002/cbic.202100054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/26/2021] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology has been widely applied for nucleic acid detection because of its high specificity. By using the highly specific and irreversible bond between HaloTag and its alkane chlorine ligand, we modified dCas9 (deactivated CRISPR/Cas9) with biotin as a biosensor to detect nucleic acids. The CRISPR biosensor was facilely prepared to adequately maintain its DNA-recognition capability. Furthermore, by coupling biolayer interferometry (BLI) with the CRISPR biosensor, a real-time, sensitive, and rapid digital system called CRISPR-BLI was established for the detection of double-stranded DNA. The CRISPR biosensor immobilised on the biolayer could recruit the target DNA onto the biosensor surface and change its optical thickness, resulting in a shift in the interference pattern and responding signal of the BLI. The CRISPR-BLI system was further applied to detect the ALP gene of Escherichia coli DH5α combined with a polymerase chain reaction, which demonstrated a linear range from 20 to 20 000 pg and a low detection limit (1.34 pg). The CRISPR-BLI system is a promising approach for rapid and sensitive detection of target DNA analytes.
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Affiliation(s)
- Shan-Peng Qiao
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Zhen-Ni Liu
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Hai-Chao Li
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Xin He
- Department of Jilin City Institute of Biological Products, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 1228 Songjiangnan Road, Jilin, 132013, Jilin, P. R. China
| | - Hong Pan
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China
| | - Yu-Zhou Gao
- Department of Changchun Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3333 Shengbei Street, Changchun, 130052, Jilin, P. R. China.,Department of Jinan Institute of Engineering Technology, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science (CAS), 3 Gangxing Road, Jinan, 250000, Shandong, P. R. China
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18
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Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.04.08.438911. [PMID: 33851164 PMCID: PMC8043454 DOI: 10.1101/2021.04.08.438911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Despite the great promise of vaccines, the COVID-19 pandemic is ongoing and future serious outbreaks are highly likely, so that multi-pronged containment strategies will be required for many years. Nanobodies are the smallest naturally occurring single domain antigen binding proteins identified to date, possessing numerous properties advantageous to their production and use. We present a large repertoire of high affinity nanobodies against SARS-CoV-2 Spike protein with excellent kinetic and viral neutralization properties, which can be strongly enhanced with oligomerization. This repertoire samples the epitope landscape of the Spike ectodomain inside and outside the receptor binding domain, recognizing a multitude of distinct epitopes and revealing multiple neutralization targets of pseudoviruses and authentic SARS-CoV-2, including in primary human airway epithelial cells. Combinatorial nanobody mixtures show highly synergistic activities, and are resistant to mutational escape and emerging viral variants of concern. These nanobodies establish an exceptional resource for superior COVID-19 prophylactics and therapeutics.
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Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Natalia E Ketaren
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Erica Y Jacobs
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Jean Paul Olivier
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Tanmoy Sanyal
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Magda Rutkowska
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nicolas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sarah Keegan
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Jacob B Jiler
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Milana E Stein
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Theodora Hatziioannou
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
| | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, NY, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, New York 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York 10065, USA
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19
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Epitope Binning of Novel Monoclonal Anti F1 and Anti LcrV Antibodies and Their Application in a Simple, Short, HTRF Test for Clinical Plague Detection. Pathogens 2021; 10:pathogens10030285. [PMID: 33801490 PMCID: PMC8001648 DOI: 10.3390/pathogens10030285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 11/18/2022] Open
Abstract
Mouse monoclonal antibodies were raised against plague disease biomarkers: the bacterial capsular protein fraction 1 (F1) and the low-calcium response—LcrV virulence factor (Vag). A novel tandem assay, employing BioLayer Interferometry (BLI), enabled the isolation of antibodies against four different epitopes on Vag. The tandem assay was carried out with hybridoma supernatants, circumventing the need for antibody purification. The BioLayer assay was further adopted for characterization of epitope-repetitive antigens, enabling the discovery of two unique epitopes on F1. The selected antibodies were purified and applied as “oligo-clonal” reagents for the immuno-detection of both biomarkers. The developed Homogenous Time Resolved Fluorescence (HTRF) tests were short (10 min) and simple (no washing steps), allowing for detection of 10 ng/mL F1 and 2.5 ng/mL Vag. The tests were successfully applied for detection of disease biomarkers produced by various Y. pestis strains during growth in blood culture vials.
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20
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Turner BL, Kilgour KM, Stine SJ, Daniele M, Menegatti S. Dual-Affinity Ratiometric Quenching (DARQ) Assay for the Quantification of Therapeutic Antibodies in CHO-S Cell Culture Fluids. Anal Chem 2020; 92:16274-16283. [DOI: 10.1021/acs.analchem.0c04269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Brendan L. Turner
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, North Carolina 27695, United States
| | - Katie M. Kilgour
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina 27695, United States
| | - Sydney J. Stine
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina 27695, United States
| | - Michael Daniele
- Joint Department of Biomedical Engineering, North Carolina State University and University of North Carolina at Chapel Hill, 911 Oval Drive, Raleigh, North Carolina 27695, United States
- Department of Electrical & Computer Engineering, North Carolina State University, 890 Oval Drive, Raleigh, North Carolina 27695, United States
| | - Stefano Menegatti
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners Way, Raleigh, North Carolina 27695, United States
- Biomanufacturing Training and Education Center (BTEC), 850 Oval Drive, Raleigh, North Carolina 27606, United States
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21
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Native high-resolution mass spectrometry analysis of noncovalent protein complexes up to 450 kDa. Bioanalysis 2020; 12:1353-1362. [PMID: 32830519 DOI: 10.4155/bio-2020-0145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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22
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Brooks BD, Closmore A, Yang J, Holland M, Cairns T, Cohen GH, Bailey-Kellogg C. Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition. Molecules 2020; 25:molecules25163659. [PMID: 32796656 PMCID: PMC7464469 DOI: 10.3390/molecules25163659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
Vaccines and immunotherapies depend on the ability of antibodies to sensitively and specifically recognize particular antigens and specific epitopes on those antigens. As such, detailed characterization of antibody-antigen binding provides important information to guide development. Due to the time and expense required, high-resolution structural characterization techniques are typically used sparingly and late in a development process. Here, we show that antibody-antigen binding can be characterized early in a process for whole panels of antibodies by combining experimental and computational analyses of competition between monoclonal antibodies for binding to an antigen. Experimental "epitope binning" of monoclonal antibodies uses high-throughput surface plasmon resonance to reveal which antibodies compete, while a new complementary computational analysis that we call "dock binning" evaluates antibody-antigen docking models to identify why and where they might compete, in terms of possible binding sites on the antigen. Experimental and computational characterization of the identified antigenic hotspots then enables the refinement of the competitors and their associated epitope binding regions on the antigen. While not performed at atomic resolution, this approach allows for the group-level identification of functionally related monoclonal antibodies (i.e., communities) and identification of their general binding regions on the antigen. By leveraging extensive epitope characterization data that can be readily generated both experimentally and computationally, researchers can gain broad insights into the basis for antibody-antigen recognition in wide-ranging vaccine and immunotherapy discovery and development programs.
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Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58102, USA
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
- Correspondence: ; Tel.: +1-435-222-1403
| | - Adam Closmore
- Department of Pharmacy, North Dakota State University, Fargo, ND 58102, USA;
| | - Juechen Yang
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Michael Holland
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Tina Cairns
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
| | - Gary H. Cohen
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
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Brown ME, Bedinger D, Lilov A, Rathanaswami P, Vásquez M, Durand S, Wallace-Moyer I, Zhong L, Nett JH, Burnina I, Caffry I, Lynaugh H, Sinclair M, Sun T, Bukowski J, Xu Y, Abdiche YN. Assessing the binding properties of the anti-PD-1 antibody landscape using label-free biosensors. PLoS One 2020; 15:e0229206. [PMID: 32134960 PMCID: PMC7058304 DOI: 10.1371/journal.pone.0229206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/31/2020] [Indexed: 12/21/2022] Open
Abstract
Here we describe an industry-wide collaboration aimed at assessing the binding properties of a comprehensive panel of monoclonal antibodies (mAbs) against programmed cell death protein 1 (PD-1), an important checkpoint protein in cancer immunotherapy and validated therapeutic target, with well over thirty unique mAbs either in clinical development or market-approved in the United States, the European Union or China. The binding kinetics of the PD-1/mAb interactions were measured by surface plasmon resonance (SPR) using a Carterra LSA instrument and the results were compared to data collected on a Biacore 8K. The effect of chip type on the SPR-derived binding rate constants and affinities were explored and the results compared with solution affinities from Meso Scale Discovery (MSD) and Kinetic Exclusion Assay (KinExA) experiments. When using flat chip types, the LSA and 8K platforms yielded near-identical kinetic rate and affinity constants that matched solution phase values more closely than those produced on 3D-hydrogels. Of the anti-PD-1 mAbs tested, which included a portion of those known to be in clinical development or approved, the affinities spanned from single digit picomolar to nearly 425 nM, challenging the dynamic range of our methods. The LSA instrument was also used to perform epitope binning and ligand competition studies which revealed over ten unique competitive binding profiles within this group of mAbs.
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Affiliation(s)
- Michael E. Brown
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
- * E-mail: (MEB); (YNA)
| | | | - Asparouh Lilov
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | | | - Maximiliano Vásquez
- Department of Computational Biology, Adimab, Palo Alto, CA, United States of America
| | - Stéphanie Durand
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Ian Wallace-Moyer
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Lihui Zhong
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Juergen H. Nett
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Irina Burnina
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Isabelle Caffry
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Heather Lynaugh
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Melanie Sinclair
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Tingwan Sun
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - John Bukowski
- Department of Antibody Discovery, Adimab, Lebanon, NH, United States of America
| | - Yingda Xu
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
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Anand A, Sugumaran A, Narayanasamy D. Brain targeted delivery of anticancer drugs: prospective approach using solid lipid nanoparticles. IET Nanobiotechnol 2019; 13:353-362. [PMID: 31171738 PMCID: PMC8676006 DOI: 10.1049/iet-nbt.2018.5322] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/30/2018] [Accepted: 01/28/2019] [Indexed: 04/05/2024] Open
Abstract
A brain tumour is amongst most devastating and challenging condition to overcome with suitable treatment as the drug has to cross the blood-brain barrier (BBB) with several physiological barriers like opsonisation by the reticuloendothelial system. Presently various techniques such as surgical, chemotherapeutic agents, and radiotherapy techniques have performed to extend the lifespan of patients diagnosed with glioblastoma, which did not maximise the overall survival of patients with a tumour. Nanotechnology is relied upon to diminish the requirement for intrusive methods for conveyance of therapeutics to the central nervous system. Colloidal nanocarriers sizing range 1-1000 nm have been utilised to cross BBB delivers the drug at cell levels with enhanced bioavailability and reduced toxicity. However, solid lipid nanoparticles (SLNs) are considered a highly flexible carrier for more successful remedially in brain tumour. The treatment of a brain tumour via SLNs is gaining greater potency due to its inimitable size and lipidic nature. This review focuses and represents the current strategies of SLNs in the brain tumour treatment with appropriate techniques adopted are highlighted. Based on this review, the authors concluded that SLNs embrace exclusive promising lipidic nanocarrier that could be utilised to target a brain tumour effectively.
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Affiliation(s)
- Anupriya Anand
- Department of Pharmaceutics, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, India
| | - Abimanyu Sugumaran
- Department of Pharmaceutics, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, India.
| | - Damodharan Narayanasamy
- Department of Pharmaceutics, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, India
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25
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Wollacott AM, Robinson LN, Ramakrishnan B, Tissire H, Viswanathan K, Shriver Z, Babcock GJ. Structural prediction of antibody-APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data. J Mol Recognit 2019; 32:e2778. [DOI: 10.1002/jmr.2778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/21/2018] [Accepted: 12/06/2018] [Indexed: 12/29/2022]
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26
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Tang F, LeBlanc ME, Wang W, Liang D, Chen P, Chou TH, Tian H, Li W. Anti-secretogranin III therapy of oxygen-induced retinopathy with optimal safety. Angiogenesis 2019; 22:369-382. [PMID: 30644010 DOI: 10.1007/s10456-019-09662-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/07/2019] [Indexed: 12/17/2022]
Abstract
Retinopathy of prematurity (ROP) with pathological retinal neovascularization is the most common cause of blindness in children. ROP is currently treated with laser therapy or cryotherapy, both of which may adversely affect the peripheral vision with limited efficacy. Owing to the susceptibility of the developing retina and vasculatures to pharmacological intervention, there is currently no approved drug therapy for ROP in preterm infants. Secretogranin III (Scg3) was recently discovered as a highly disease-restricted angiogenic factor, and a Scg3-neutralizing monoclonal antibody (mAb) was reported with high efficacy to alleviate oxygen-induced retinopathy (OIR) in mice, a surrogate model of ROP. Herein we independently investigated the efficacy of anti-Scg3 mAb in OIR mice and characterized its safety in neonatal mice. We developed a new Scg3-neutralizing mAb recognizing a distinct epitope and independently established the therapeutic activity of anti-Scg3 therapy to alleviate OIR-induced pathological retinal neovascularization in mice. Importantly, anti-Scg3 mAb showed no detectable adverse effects on electroretinography and developing retinal vasculature. Furthermore, systemic anti-Scg3 mAb induced no renal tubular injury or abnormality in kidney vessel development and body weight gain of neonatal mice. In contrast, anti-vascular endothelial growth factor drug aflibercept showed significant side effects in neonatal mice. These results suggest that anti-Scg3 mAb may have the safety and efficacy profiles required for ROP therapy.
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Affiliation(s)
- Fen Tang
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Michelle E LeBlanc
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Weiwen Wang
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Dan Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Ping Chen
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
- Department of Ophthalmology, Renji Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Tsung-Han Chou
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Hong Tian
- Everglades Biopharma, LLC, Miami, FL, USA
| | - Wei Li
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA.
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Theunissen JW, Cai AG, Bhatti MM, Cooper AB, Avery AD, Dorfman R, Guelman S, Levashova Z, Migone TS. Treating Tissue Factor-Positive Cancers with Antibody-Drug Conjugates That Do Not Affect Blood Clotting. Mol Cancer Ther 2018; 17:2412-2426. [PMID: 30126944 DOI: 10.1158/1535-7163.mct-18-0471] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/21/2018] [Accepted: 08/14/2018] [Indexed: 11/16/2022]
Abstract
The primary function of tissue factor (TF) resides in the vasculature as a cofactor of blood clotting; however, multiple solid tumors aberrantly express this transmembrane receptor on the cell surface. Here, we developed anti-TF antibody-drug conjugates (ADC) that did not interfere with the coagulation cascade and benchmarked them against previously developed anti-TF ADCs. After screening an affinity-matured antibody panel of diverse paratopes and affinities, we identified one primary paratope family that did not inhibit conversion of Factor X (FX) to activated Factor X (FXa) and did not affect conversion of prothrombin to thrombin. The rest of the antibody panel and previously developed anti-TF antibodies were found to perturb coagulation to varying degrees. To compare the anticancer activity of coagulation-inert and -inhibitory antibodies as ADCs, a selection of antibodies was conjugated to the prototypic cytotoxic agent monomethyl auristatin E (MMAE) through a protease-cleavable linker. The coagulation-inert and -inhibitory anti-TF ADCs both killed cancer cells effectively. Importantly, the coagulation-inert ADCs were as efficacious as tisotumab vedotin, a clinical stage ADC that affected blood clotting, including in patient-derived xenografts from three solid tumor indications with a need for new therapeutic treatments-squamous cell carcinoma of the head and neck (SCCHN), ovarian, and gastric adenocarcinoma. Furthermore, a subset of the anti-TF antibodies could also be considered for the treatment of other diseases associated with upregulation of membranous TF expression, such as macular degeneration. Mol Cancer Ther; 17(11); 2412-26. ©2018 AACR.
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Affiliation(s)
| | - Allen G Cai
- Iconic Therapeutics, South San Francisco, California
| | | | | | | | - Ryan Dorfman
- Haematologic Technologies, Essex Junction, Vermont
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28
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Vanhove E, Vanhove M. Affinity determination of biomolecules: a kinetic model for the analysis of pre-equilibrium titration curves. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:961-966. [DOI: 10.1007/s00249-018-1318-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/13/2018] [Accepted: 07/03/2018] [Indexed: 11/29/2022]
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Optimizing NBE PK/PD assays using the Gyrolab Affinity Software; conveniently within the bioanalyst's existing workflow. Bioanalysis 2018; 10:397-406. [DOI: 10.4155/bio-2017-0251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: The fully automated microfluidics-based Gyrolab is a popular instrument for the bioanalysis of protein therapeutics; requiring minimal sample and reagent volumes. Gyros offers affinity software for determining binding affinity in solution using a high-throughput method and miniaturized reactions. Results: Using this affinity software, multiple CTGF-targeting reagents were characterized on the Gyrolab after <100% target coverage was seen in a cynomolgus pharmacokinetic/PD study dosed with anti-CTGF antibodies. The results uncovered magnitude differences in binding affinities between the dosed antibody, target and assay reagents. Conclusion: The binding affinity values were used to investigate reduced target coverage and results highlight potential of the affinity software for incorporation into the bioanalyst's existing Gyrolab workflow for characterizing reagents and optimizing pharmacokinetic/PD bioanalytical assays.
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30
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Streamlined circular proximity ligation assay provides high stringency and compatibility with low-affinity antibodies. Proc Natl Acad Sci U S A 2018; 115:E925-E933. [PMID: 29339495 DOI: 10.1073/pnas.1718283115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proximity ligation assay (PLA) is a powerful tool for quantitative detection of protein biomarkers in biological fluids and tissues. Here, we present the circular proximity ligation assay (c-PLA), a highly specific protein detection method that outperforms traditional PLA in stringency, ease of use, and compatibility with low-affinity reagents. In c-PLA, two proximity probes bind to an analyte, providing a scaffolding that positions two free oligonucleotides such that they can be ligated into a circular DNA molecule. This assay format stabilizes antigen proximity probe complexes and enhances stringency by reducing the probability of random background ligation events. Circle formation also increases selectivity, since the uncircularized DNA can be removed enzymatically. We compare this method with traditional PLA on several biomarkers and show that the higher stringency for c-PLA improves reproducibility and enhances sensitivity in both buffer and human plasma. The limit of detection ranges from femtomolar to nanomolar concentrations for both methods. Kinetic analyses using surface plasmon resonance (SPR) and biolayer interferometry (BLI) reveal that the variation in limit of detection is due to the variation in antibody affinity and that c-PLA outperforms traditional PLA for low-affinity antibodies. The lower background signal can be used to increase proximity probe concentration while maintaining a high signal-to-noise ratio, thereby enabling the use of low-affinity reagents in a homogeneous assay format. We anticipate that the advantages of c-PLA will be useful in a variety of clinical protein detection applications where high-affinity reagents are lacking.
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31
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Li M, Guo X, Li H, Zuo X, Hao R, Song H, Aldalbahi A, Ge Z, Li J, Li Q, Song S, Li S, Shao N, Fan C, Wang L. Epitope Binning Assay Using an Electron Transfer-Modulated Aptamer Sensor. ACS APPLIED MATERIALS & INTERFACES 2018; 10:341-349. [PMID: 29241329 DOI: 10.1021/acsami.7b17324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Surface plasmon resonance and quartz crystal microbalance are workhorses of protein-DNA interaction research for over 20 years, providing ways to quantitatively determine the protein-DNA binding. However, the cost, necessary technical expertise, and severe nonspecific adsorption poses barriers to their use. Convenient and effective techniques for the measurement of protein-DNA binding affinity and the epitope binning between DNA and proteins for developing highly sensitive detection platform remain challenging. Here, we develop a binding-induced alteration in electron transfer kinetics of the redox reporter labeled (methylene blue) on DNA aptamer to measure the binding affinity between prostate-specific antigen (PSA) and aptamer. We demonstrate that the binding of PSA to aptamer decreases the electron transfer rate of methylene blue for ∼45%. Further, we identify the best pairwise selection of aptamers for developing sandwich assay by sorting from 10 pairwise modes with the PSA detection limit of 500 ng/mL. Our study provides promising ways to analyze the binding affinity between ligand and receptor and to sort pairwise between aptamers or antibodies for the development of highly sensitive sandwich immunoassays.
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Affiliation(s)
- Min Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xudong Guo
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Hui Li
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Rongzhang Hao
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Hongbin Song
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Zhilei Ge
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Shaohua Li
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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32
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Yang NJ, Kauke MJ, Sun F, Yang LF, Maass KF, Traxlmayr MW, Yu Y, Xu Y, Langer RS, Anderson DG, Wittrup KD. Cytosolic delivery of siRNA by ultra-high affinity dsRNA binding proteins. Nucleic Acids Res 2017. [PMID: 28641400 PMCID: PMC5570165 DOI: 10.1093/nar/gkx546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Protein-based methods of siRNA delivery are capable of uniquely specific targeting, but are limited by technical challenges such as low potency or poor biophysical properties. Here, we engineered a series of ultra-high affinity siRNA binders based on the viral protein p19 and developed them into siRNA carriers targeted to the epidermal growth factor receptor (EGFR). Combined in trans with a previously described endosome-disrupting agent composed of the pore-forming protein Perfringolysin O (PFO), potent silencing was achieved in vitro with no detectable cytotoxicity. Despite concerns that excessively strong siRNA binding could prevent the discharge of siRNA from its carrier, higher affinity continually led to stronger silencing. We found that this improvement was due to both increased uptake of siRNA into the cell and improved pharmacodynamics inside the cell. Mathematical modeling predicted the existence of an affinity optimum that maximizes silencing, after which siRNA sequestration decreases potency. Our study characterizing the affinity dependence of silencing suggests that siRNA-carrier affinity can significantly affect the intracellular fate of siRNA and may serve as a handle for improving the efficiency of delivery. The two-agent delivery system presented here possesses notable biophysical properties and potency, and provide a platform for the cytosolic delivery of nucleic acids.
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Affiliation(s)
- Nicole J Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Monique J Kauke
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fangdi Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucy F Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Katie F Maass
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael W Traxlmayr
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yao Yu
- Protein Analytics, Adimab LLC, Lebanon, NH 03766, USA
| | - Yingda Xu
- Protein Analytics, Adimab LLC, Lebanon, NH 03766, USA
| | - Robert S Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - K Dane Wittrup
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Fang Y, Chu TH, Ackerman ME, Griswold KE. Going native: Direct high throughput screening of secreted full-length IgG antibodies against cell membrane proteins. MAbs 2017; 9:1253-1261. [PMID: 28933630 PMCID: PMC5680790 DOI: 10.1080/19420862.2017.1381812] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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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König F, Schubert T, Längst G. The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences. PLoS One 2017; 12:e0178875. [PMID: 28594954 PMCID: PMC5464589 DOI: 10.1371/journal.pone.0178875] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/20/2017] [Indexed: 12/15/2022] Open
Abstract
The monoclonal antibody S9.6 is a widely-used tool to purify, analyse and quantify R-loop structures in cells. A previous study using the surface plasmon resonance technology and a single-chain variable fragment (scFv) of S9.6 showed high affinity (0.6 nM) for DNA—RNA and also a high affinity (2.7 nM) for RNA—RNA hybrids. We used the microscale thermophoresis method allowing surface independent interaction studies and electromobility shift assays to evaluate additional RNA-DNA hybrid sequences and to quantify the binding affinities of the S9.6 antibody with respect to distinct sequences and their GC-content. Our results confirm high affinity binding to previously analysed sequences, but reveals that binding affinities are highly sequence specific. Our study presents R-loop sequences that independent of GC-content and in different sequence variations exhibit either no binding, binding affinities in the micromolar range and as well high affinity binding in the nanomolar range. Our study questions the usefulness of the S9.6 antibody in the quantitative analysis of R-loop sequences in vivo.
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Affiliation(s)
- Fabian König
- Biochemistry III; Biochemistry Centre Regensburg (BCR), University of Regensburg, Universitätsstr, Regensburg, Germany
| | - Thomas Schubert
- Biochemistry III; Biochemistry Centre Regensburg (BCR), University of Regensburg, Universitätsstr, Regensburg, Germany
- 2Bind GmbH, Regensburg, Germany
| | - Gernot Längst
- Biochemistry III; Biochemistry Centre Regensburg (BCR), University of Regensburg, Universitätsstr, Regensburg, Germany
- * E-mail:
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Cell Attachment Domains of the Porcine Epidemic Diarrhea Virus Spike Protein Are Key Targets of Neutralizing Antibodies. J Virol 2017; 91:JVI.00273-17. [PMID: 28381581 DOI: 10.1128/jvi.00273-17] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/24/2017] [Indexed: 01/12/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) causes enteric disease in pigs, resulting in significant economic losses to the swine industry worldwide. Current vaccination approaches against this emerging coronavirus are only partially effective, though natural infection protects pigs against reinfection and provides lactogenic immunity to suckling piglets. The viral spike (S) glycoprotein, responsible for receptor binding and cell entry, is the major target for neutralizing antibodies. However, knowledge of antibody epitopes, their nature and location in the spike structure, and the mechanisms by which the antibodies interfere with infection is scarce. Here we describe the generation and characterization of 10 neutralizing and nonneutralizing mouse monoclonal antibodies raised against the S1 receptor binding subunit of the S protein. By expression of different S1 protein fragments, six antibody epitope classes distributed over the five structural domains of the S1 subunit were identified. Characterization of antibodies for cross-reactivity and cross-neutralization revealed antigenic differences among PEDV strains. The epitopes of potent neutralizing antibodies segregated into two epitope classes and mapped within the N-terminal sialic acid binding domain and in the more C-terminal receptor binding domain. Antibody neutralization escape mutants displayed single amino acid substitutions that impaired antibody binding and neutralization and defined the locations of the epitopes. Our observations picture the antibody epitope landscape of the PEDV S1 subunit and reveal that its cell attachment domains are key targets of neutralizing antibodies.IMPORTANCE Porcine epidemic diarrhea virus (PEDV), an emerging porcine coronavirus, causes an economically important enteric disease in pigs. Effective PEDV vaccines for disease control are currently lacking. The spike (S) glycoprotein on the virion surface is the key player in virus cell entry and, therefore, the main target of neutralizing antibodies. To understand the antigenic landscape of the PEDV spike protein, we developed monoclonal antibodies against the spike protein's S1 receptor binding region and characterized their epitopes, neutralizing activity, and cross-reactivity toward multiple PEDV strains. Epitopes of antibodies segregated into six epitope classes dispersed over the multidomain S1 structure. Monoclonal antibodies revealed antigenic variability in B-cell epitopes between PEDV strains. The epitopes of neutralizing antibodies mapped to two distinct domains in S1 that are involved in binding to carbohydrate and proteinaceous cell surface molecules, respectively, indicating the importance of these cell attachment sites on the PEDV spike protein in eliciting a protective humoral immune response.
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Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis. Sci Rep 2016; 6:39774. [PMID: 28008969 PMCID: PMC5180089 DOI: 10.1038/srep39774] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/28/2016] [Indexed: 12/19/2022] Open
Abstract
High-quality immunoreagents enhance the performance and reproducibility of immunoassays and, in turn, the quality of both biological and clinical measurements. High quality recombinant immunoreagents are generated using antibody-phage display. One metric of antibody quality – the binding affinity – is quantified through the dissociation constant (KD) of each recombinant antibody and the target antigen. To characterize the KD of recombinant antibodies and target antigen, we introduce affinity electrophoretic mobility shift assays (EMSAs) in a high-throughput format suitable for small volume samples. A microfluidic card comprised of free-standing polyacrylamide gel (fsPAG) separation lanes supports 384 concurrent EMSAs in 30 s using a single power source. Sample is dispensed onto the microfluidic EMSA card by acoustic droplet ejection (ADE), which reduces EMSA variability compared to sample dispensing using manual or pin tools. The KD for each of a six-member fragment antigen-binding fragment library is reported using ~25-fold less sample mass and ~5-fold less time than conventional heterogeneous assays. Given the form factor and performance of this micro- and mesofluidic workflow, we have developed a sample-sparing, high-throughput, solution-phase alternative for biomolecular affinity characterization.
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Patel CN, Bauer SP, Davies J, Durbin JD, Shiyanova TL, Zhang K, Tang JX. N+1 Engineering of an Aspartate Isomerization Hotspot in the Complementarity-Determining Region of a Monoclonal Antibody. J Pharm Sci 2016; 105:512-518. [PMID: 26869414 DOI: 10.1016/s0022-3549(15)00185-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 01/22/2023]
Abstract
Aspartate (Asp) isomerization is a common degradation pathway and a potential critical quality attribute that needs to be well characterized during the optimization and development of therapeutic antibodies. A putative Asp-serine (Ser) isomerization motif was identified in the complementarity-determining region of a humanized monoclonal antibody and shown to be a developability risk using accelerated stability analyses. To address this issue, we explored different antibody engineering strategies. Direct engineering of the Asp residue resulted in a greater than 5× loss of antigen-binding affinity and bioactivity, indicating a critical role for this residue. In contrast, rational engineering of the Ser residue at the n+1 position had a negligible impact on antigen binding affinity and bioactivity compared with the parent molecule. Furthermore, the n+1 engineering strategy effectively eliminated Asp isomerization as determined by accelerated stability analysis. This outcome affirms that the rate of Asp isomerization is strongly dependent on the identity of the n+1 residue. This report highlights a systematic antibody engineering strategy for mitigating an Asp isomerization developability risk during lead optimization.
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Affiliation(s)
- Chetan N Patel
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285.
| | - Scott P Bauer
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285
| | - Julian Davies
- Lilly Biotechnology Center, Biotechnology Discovery Research, Eli Lilly and Company, San Diego, California 92121
| | - Jim D Durbin
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285
| | - Tatiyana L Shiyanova
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285
| | - Kai Zhang
- Lilly Biotechnology Center, Biotechnology Discovery Research, Eli Lilly and Company, San Diego, California 92121
| | - Jason X Tang
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285
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38
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Veugelen S, Dewilde M, De Strooper B, Chávez-Gutiérrez L. Screening and Characterization Strategies for Nanobodies Targeting Membrane Proteins. Methods Enzymol 2016; 584:59-97. [PMID: 28065273 DOI: 10.1016/bs.mie.2016.10.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The study of membrane protein function and structure requires their successful detection, expression, solubilization, and/or reconstitution, which poses a challenging task and relies on the availability of suitable tools. Several research groups have successfully applied Nanobodies in the purification, as well as the functional and structural characterization of membrane proteins. Nanobodies are small, single-chain antibody fragments originating from camelids presenting on average a longer CDR3 which enables them to bind in cavities and clefts (such as active and allosteric sites). Notably, Nanobodies generally bind conformational epitopes making them very interesting tools to stabilize, dissect, and characterize specific protein conformations. In the clinic, several Nanobodies are under evaluation either as potential drug candidates or as diagnostic tools. In recent years, we have successfully generated high-affinity, conformation-sensitive anti-γ-secretase Nanobodies. γ-Secretase is a multimeric membrane protease involved in processing of the amyloid precursor protein with high clinical relevance as mutations in its catalytic subunit (Presenilin) cause early-onset Alzheimer's disease. Advancing our knowledge on the mechanisms governing γ-secretase intramembrane proteolysis through various strategies may lead to novel therapeutic avenues for Alzheimer's disease. In this chapter, we present the strategies we have developed and applied for the screening and characterization of anti-γ-secretase Nanobodies. These protocols could be of help in the generation of Nanobodies targeting other membrane proteins.
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Affiliation(s)
- S Veugelen
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium
| | - M Dewilde
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium
| | - B De Strooper
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium; UCL Institute of Neurology, London, United Kingdom
| | - L Chávez-Gutiérrez
- University of Leuven, Leuven, Belgium; VIB Center for Brain and Disease, Leuven, Belgium.
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39
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Kelly RL, Yu Y, Sun T, Caffry I, Lynaugh H, Brown M, Jain T, Xu Y, Wittrup KD. Target-independent variable region mediated effects on antibody clearance can be FcRn independent. MAbs 2016; 8:1269-1275. [PMID: 27610650 DOI: 10.1080/19420862.2016.1208330] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The importance of the neonatal Fc receptor (FcRn) in extending the serum half-life of monoclonal antibodies (mAbs) is well demonstrated, and has led to the development of multiple engineering approaches designed to alter Fc interactions with FcRn. Recent reports have additionally highlighted the effect of nonspecific interactions on antibody pharmacokinetics (PK), suggesting an FcRn-independent mechanism for mAb clearance. In this report we examine a case study of 2 anti-interleukin-12/23 antibodies, ustekinumab and briakinumab, which share the same target and Fc, but differ in variable region sequences. Ustekinumab displayed near baseline signal in a wide range of early stage developability assays for undesirable protein/protein interactions, while briakinumab showed significant propensity for self- and cross-interactions. This phenotypic difference correlates with faster clearance rates for briakinumab in both human FcRn transgenic and FcRn knockout mice. These findings support a dominant contribution for FcRn-independent clearance for antibodies with high nonspecificity, and highlight a key role for early stage developability screening to eliminate clones with such high nonspecific disposition PK.
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Affiliation(s)
- Ryan L Kelly
- a Department of Biological Engineering , Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Yao Yu
- b Protein Analytics , Adimab , Lebanon , NH , USA
| | - Tingwan Sun
- b Protein Analytics , Adimab , Lebanon , NH , USA
| | | | | | | | - Tushar Jain
- c Computational Biology , Adimab , Palo Alto , CA , USA
| | - Yingda Xu
- d Department of Chemical Engineering, Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - K Dane Wittrup
- a Department of Biological Engineering , Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge , MA , USA.,d Department of Chemical Engineering, Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , MA , USA
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40
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Chan YN, Boesch AW, Osei-Owusu NY, Emileh A, Crowley AR, Cocklin SL, Finstad SL, Linde CH, Howell RA, Zentner I, Cocklin S, Miles AR, Eckman JW, Alter G, Schmitz JE, Ackerman ME. IgG Binding Characteristics of Rhesus Macaque FcγR. THE JOURNAL OF IMMUNOLOGY 2016; 197:2936-47. [PMID: 27559046 DOI: 10.4049/jimmunol.1502252] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 07/26/2016] [Indexed: 11/19/2022]
Abstract
Indian rhesus macaques (Macaca mulatta) are routinely used in preclinical studies to evaluate therapeutic Abs and candidate vaccines. The efficacy of these interventions in many cases is known to rely heavily on the ability of Abs to interact with a set of Ab FcγR expressed on innate immune cells. Yet, despite their presumed functional importance, M. mulatta Ab receptors are largely uncharacterized, posing a fundamental limit to ensuring accurate interpretation and translation of results from studies in this model. In this article, we describe the binding characteristics of the most prevalent allotypic variants of M. mulatta FcγR for binding to both human and M. mulatta IgG of varying subclasses. The resulting determination of the affinity, specificity, and glycan sensitivity of these receptors promises to be useful in designing and evaluating studies of candidate vaccines and therapeutic Abs in this key animal model and exposes significant evolutionary divergence between humans and macaques.
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Affiliation(s)
- Ying N Chan
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Austin W Boesch
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Nana Y Osei-Owusu
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH 03755
| | - Ali Emileh
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Andrew R Crowley
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH 03755
| | - Sarah L Cocklin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Samantha L Finstad
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Caitlyn H Linde
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Rebecca A Howell
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Isaac Zentner
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Simon Cocklin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102
| | - Adam R Miles
- Wasatch Microfluidics, Salt Lake City, UT 84103; and
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
| | - Joern E Schmitz
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115
| | - Margaret E Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755; Molecular and Cellular Biology Program, Dartmouth College, Hanover, NH 03755;
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41
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Badarau A, Rouha H, Malafa S, Battles MB, Walker L, Nielson N, Dolezilkova I, Teubenbacher A, Banerjee S, Maierhofer B, Weber S, Stulik L, Logan DT, Welin M, Mirkina I, Pleban C, Zauner G, Gross K, Jägerhofer M, Magyarics Z, Nagy E. Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies. MAbs 2016; 8:1347-1360. [PMID: 27467113 PMCID: PMC5058624 DOI: 10.1080/19420862.2016.1215791] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
LukGH (LukAB) is a potent leukocidin of Staphylococcus aureus that lyses human phagocytic cells and is thought to contribute to immune evasion. Unlike the other bi-component leukocidins of S. aureus, LukGH forms a heterodimer before binding to its receptor, CD11b expressed on professional phagocytic cells, and displays significant sequence variation. We employed a high diversity human IgG1 library presented on yeast cells to discover monoclonal antibodies (mAbs) neutralizing the cytolytic activity of LukGH. Recombinant LukG and LukH monomers or a LukGH dimer were used as capture antigens in the library selections. We found that mAbs identified with LukG or LukH as bait had no or very low toxin neutralization potency. In contrast, LukGH dimer-selected antibodies proved to be highly potent, and several mAbs were able to neutralize even the most divergent LukGH variants. Based on biolayer interferometry and mesoscale discovery, the high affinity antibody binding site on the LukGH complex was absent on the individual monomers, suggesting that it was generated upon formation of the LukG-LukH dimer. X-ray crystallography analysis of the complex between the LukGH dimer and the antigen-binding fragment of a very potent mAb (PDB code 5K59) indicated that the epitope is located in the predicted cell binding region (rim domain) of LukGH. The corresponding IgG inhibited the binding of LukGH dimer to target cells. Our data suggest that knowledge of the native conformation of target molecules is essential to generate high affinity and functional mAbs.
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Affiliation(s)
- Adriana Badarau
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Harald Rouha
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Stefan Malafa
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | | | | | | | | | - Srijib Banerjee
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | - Susanne Weber
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Lukas Stulik
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Derek T Logan
- c SARomics Biostructures AB , Medicon Village, Lund , Sweden
| | - Martin Welin
- c SARomics Biostructures AB , Medicon Village, Lund , Sweden
| | - Irina Mirkina
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Clara Pleban
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Gerhild Zauner
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Karin Gross
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | | | - Zoltán Magyarics
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
| | - Eszter Nagy
- a Arsanis Biosciences , Campus Vienna Biocenter, Vienna , Austria
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42
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Kelly RL, Sun T, Jain T, Caffry I, Yu Y, Cao Y, Lynaugh H, Brown M, Vásquez M, Wittrup KD, Xu Y. High throughput cross-interaction measures for human IgG1 antibodies correlate with clearance rates in mice. MAbs 2016; 7:770-7. [PMID: 26047159 PMCID: PMC4622737 DOI: 10.1080/19420862.2015.1043503] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Although improvements in technology for the isolation of potential therapeutic antibodies have made the process increasingly predictable, the development of biologically active monoclonal antibodies (mAbs) into drugs can often be impeded by developability issues such as poor expression, solubility, and promiscuous cross-reactivity. Establishing early stage developability screening assays capable of predicting late stage behavior is therefore of high value to minimize development risks. Toward this goal, we selected a panel of 16 monoclonal antibodies (mAbs) representing different developability profiles, in terms of self- and cross-interaction propensity, and examined their downstream behavior from expression titer to accelerated stability and pharmacokinetics in mice. Clearance rates showed significant rank-order correlations to 2 cross-interaction related assays, with the closest correlation to a non-specificity assay on the surface of yeast. Additionally, 2 self-association assays correlated with each other but not to mouse clearance rate. This case study suggests that combining assays capable of high throughput screening of self- and cross-interaction early in the discovery stage could significantly lower downstream development risks.
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Affiliation(s)
- Ryan L Kelly
- a Department of Biological Engineering; Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology ; Cambridge , MA , USA
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43
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Jalali-Yazdi F, Huong Lai L, Takahashi TT, Roberts RW. High-Throughput Measurement of Binding Kinetics by mRNA Display and Next-Generation Sequencing. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Farzad Jalali-Yazdi
- Department of Chemical Engineering and Materials Science; University of Southern California; Los Angeles CA 90089 USA
| | - Lan Huong Lai
- Department of Chemistry; University of Southern California; Los Angeles CA 90089 USA
| | - Terry T. Takahashi
- Department of Chemistry; University of Southern California; Los Angeles CA 90089 USA
| | - Richard W. Roberts
- Department of Chemical Engineering and Materials Science; University of Southern California; Los Angeles CA 90089 USA
- Department of Molecular Computational Biology; USC Norris Comprehensive Cancer Center; University of Southern California; Los Angeles CA 90089 USA
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44
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Jalali-Yazdi F, Lai LH, Takahashi TT, Roberts RW. High-Throughput Measurement of Binding Kinetics by mRNA Display and Next-Generation Sequencing. Angew Chem Int Ed Engl 2016; 55:4007-10. [PMID: 26914638 DOI: 10.1002/anie.201600077] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/02/2016] [Indexed: 01/23/2023]
Abstract
There is great demand for high-throughput methods to characterize ligand affinity. By combining mRNA display with next-generation sequencing, we determined the kinetic on- and off-rates for over twenty thousand ligands without the need for synthesis or purification of individual members. Our results are reproducible and as accurate as those obtained with other methods of affinity measurement.
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Affiliation(s)
- Farzad Jalali-Yazdi
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Lan Huong Lai
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Terry T Takahashi
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Richard W Roberts
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA. .,Department of Molecular Computational Biology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA.
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45
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Pogoutse AK, Lai CCL, Ostan N, Yu RH, Schryvers AB, Moraes TF. A method for measuring binding constants using unpurified in vivo biotinylated ligands. Anal Biochem 2016; 501:35-43. [PMID: 26898305 DOI: 10.1016/j.ab.2016.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 11/26/2022]
Abstract
Obtaining accurate kinetics and steady-state binding constants for biomolecular interactions normally requires pure and homogeneous protein preparations. Furthermore, in many cases, one of the ligands must be labeled. Over the past decade, several technologies have been introduced that allow for the measurement of kinetics constants for multiple different interactions in parallel. One such technology is bio-layer interferometry (BLI), which has been used to develop systems that can measure up to 96 biomolecular interactions simultaneously. However, despite the ever-increasing throughput of the tools available for measuring protein-protein interactions, the preparation of pure protein still remains a bottleneck in the process of producing high-quality kinetics data. Here, we show that high-quality binding data can be obtained using soluble lysate fractions containing protein that has been biotinylated in vivo using BirA and then applied to BLI sensors without further purification. Furthermore, we show that BirA ligase does not necessarily need to be co-overexpressed with the protein of interest for biotinylation of the biotin acceptor peptide to occur, suggesting that the activity of endogenous BirA in Escherichia coli is sufficient for producing enough biotinylated protein for a binding experiment.
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Affiliation(s)
| | | | - Nicholas Ostan
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Rong-hua Yu
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Anthony B Schryvers
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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46
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Yu Y, Mitchell S, Lynaugh H, Brown M, Nobrega RP, Zhi X, Sun T, Caffry I, Cao Y, Yang R, Burnina I, Xu Y, Estep P. Understanding ForteBio's Sensors for High-Throughput Kinetic and Epitope Screening for Purified Antibodies and Yeast Culture Supernatant. ACTA ACUST UNITED AC 2015; 21:88-95. [PMID: 26442912 PMCID: PMC4708621 DOI: 10.1177/1087057115609564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/09/2015] [Indexed: 01/26/2023]
Abstract
Real-time and label-free antibody screening systems are becoming more popular because of the increasing output of purified antibodies and antibody supernatant from many antibody discovery platforms. However, the properties of the biosensor can greatly affect the kinetic and epitope binning results generated by these label-free screening systems. ForteBio human-specific ProA, anti-human IgG quantitation (AHQ), anti-human Fc capture (AHC) sensors, and custom biotinylated-anti-human Fc capture (b-AHFc) sensors were evaluated in terms of loading ability, regeneration, kinetic characterization, and epitope binning with both purified IgG and IgG supernatant. AHC sensors proved unreliable for kinetic or binning assays at times, whereas AHQ sensors showed poor loading and regeneration abilities. ProA sensors worked well with both purified IgG and IgG supernatant. However, the interaction between ProA sensors and the Fab region of the IgG with VH3 germline limited the application of ProA sensors, especially in the epitope binning experiment. In an attempt to generate a biosensor type that would be compatible with a variety of germlines and sample types, we found that the custom b-AHFc sensors appeared to be robust working with both purified IgG and IgG supernatant, with little evidence of sensor-related artifacts.
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Affiliation(s)
- Yao Yu
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Scott Mitchell
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | | | | | | | - Xiaoyong Zhi
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Tingwan Sun
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | | | - Yuan Cao
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | - Rong Yang
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
| | | | - Yingda Xu
- Protein Analytics, Adimab, LLC, Lebanon, NH, USA
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Schröter C, Günther R, Rhiel L, Becker S, Toleikis L, Doerner A, Becker J, Schönemann A, Nasu D, Neuteboom B, Kolmar H, Hock B. A generic approach to engineer antibody pH-switches using combinatorial histidine scanning libraries and yeast display. MAbs 2015; 7:138-51. [PMID: 25523975 PMCID: PMC4622719 DOI: 10.4161/19420862.2014.985993] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
There is growing interest in the fast and robust engineering of protein pH-sensitivity that aims to reduce binding at acidic pH, compared to neutral pH. Here, we describe a novel strategy for the incorporation of pH-sensitive antigen binding functions into antibody variable domains using combinatorial histidine scanning libraries and yeast surface display. The strategy allows simultaneous screening for both, high affinity binding at pH 7.4 and pH-sensitivity, and excludes conventional negative selection steps. As proof of concept, we applied this strategy to incorporate pH-dependent antigen binding into the complementary-determining regions of adalimumab. After 3 consecutive rounds of separate heavy and light chain library screening, pH-sensitive variants could be isolated. Heavy and light chain mutations were combined, resulting in 3 full-length antibody variants that revealed sharp, reversible pH-dependent binding profiles. Dissociation rate constants at pH 6.0 increased 230- to 780-fold, while high affinity binding at pH 7.4 in the sub-nanomolar range was retained. Furthermore, binding to huFcRn and thermal stability were not affected by histidine substitutions. Overall, this study emphasizes a generalizable strategy for engineering pH-switch functions potentially applicable to a variety of antibodies and further proteins-based therapeutics.
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Affiliation(s)
- Christian Schröter
- a Institute for Organic Chemistry and Biochemistry ; Technische Universität Darmstadt ; Darmstadt , Germany
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Rouha H, Badarau A, Visram ZC, Battles MB, Prinz B, Magyarics Z, Nagy G, Mirkina I, Stulik L, Zerbs M, Jägerhofer M, Maierhofer B, Teubenbacher A, Dolezilkova I, Gross K, Banerjee S, Zauner G, Malafa S, Zmajkovic J, Maier S, Mabry R, Krauland E, Wittrup KD, Gerngross TU, Nagy E. Five birds, one stone: neutralization of α-hemolysin and 4 bi-component leukocidins of Staphylococcus aureus with a single human monoclonal antibody. MAbs 2015; 7:243-54. [PMID: 25523282 PMCID: PMC5045134 DOI: 10.4161/19420862.2014.985132] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen associated with high mortality. The emergence of antibiotic resistance and the inability of antibiotics to counteract bacterial cytotoxins involved in the pathogenesis of S. aureus call for novel therapeutic approaches, such as passive immunization with monoclonal antibodies (mAbs). The complexity of staphylococcal pathogenesis and past failures with single mAb products represent considerable barriers for antibody-based therapeutics. Over the past few years, efforts have focused on neutralizing α-hemolysin. Recent findings suggest that the concerted actions of several cytotoxins, including the bi-component leukocidins play important roles in staphylococcal pathogenesis. Therefore, we aimed to isolate mAbs that bind to multiple cytolysins by employing high diversity human IgG1 libraries presented on the surface of yeast cells. Here we describe cross-reactive antibodies with picomolar affinity for α-hemolysin and 4 different bi-component leukocidins that share only ∼26% overall amino acid sequence identity. The molecular basis of cross-reactivity is the recognition of a conformational epitope shared by α-hemolysin and F-components of gamma-hemolysin (HlgAB and HlgCB), LukED and LukSF (Panton-Valentine Leukocidin). The amino acids predicted to form the epitope are conserved and known to be important for cytotoxic activity. We found that a single cross-reactive antibody prevented lysis of human phagocytes, epithelial and red blood cells induced by α-hemolysin and leukocidins in vitro, and therefore had superior effectiveness compared to α-hemolysin specific antibodies to protect from the combined cytolytic effect of secreted S. aureus toxins. Such mAb afforded high levels of protection in murine models of pneumonia and sepsis.
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Key Words
- BLI, biolayer interferometry
- EC50, effective concentration
- Hla, α-hemolysin
- HlgAB and HlgCB, gamma-hemolysins
- IC50, inhibitory concentration
- LukED, leukocidin ED
- LukSF, leukocidin SF
- PMN, polymorphonuclear cells
- RBC, red blood cell
- Staphylococcus aureus
- engineered cross-reactivity
- exotoxins
- in vitro potency
- in vivo efficacy
- mAb, monoclonal antibody
- monoclonal antibody
- toxin neutralization
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49
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Jiang S, Hinchliffe TE, Wu T. Biomarkers of An Autoimmune Skin Disease--Psoriasis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2015; 13:224-33. [PMID: 26362816 PMCID: PMC4610974 DOI: 10.1016/j.gpb.2015.04.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/06/2015] [Accepted: 04/22/2015] [Indexed: 02/08/2023]
Abstract
Psoriasis is one of the most prevalent autoimmune skin diseases. However, its etiology and pathogenesis are still unclear. Over the last decade, omics-based technologies have been extensively utilized for biomarker discovery. As a result, some promising markers for psoriasis have been identified at the genome, transcriptome, proteome, and metabolome level. These discoveries have provided new insights into the underlying molecular mechanisms and signaling pathways in psoriasis pathogenesis. More importantly, some of these markers may prove useful in the diagnosis of psoriasis and in the prediction of disease progression once they have been validated. In this review, we summarize the most recent findings in psoriasis biomarker discovery. In addition, we will discuss several emerging technologies and their potential for novel biomarker discovery and diagnostics for psoriasis.
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Affiliation(s)
- Shan Jiang
- Department of Dermatology, Renmin Hospital of Wuhan University, Wuhan 430060, China; Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA
| | - Taylor E Hinchliffe
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA.
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50
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Solution Equilibrium Titration for High-Throughput Affinity Estimation of Unpurified Antibodies and Antibody Fragments. ACTA ACUST UNITED AC 2015; 20:1256-67. [DOI: 10.1177/1087057115595002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/14/2015] [Indexed: 01/14/2023]
Abstract
The generation of therapeutic antibodies with extremely high affinities down to the low picomolar range is today feasible with state-of-the art recombinant technologies. However, reliable and efficient identification of lead candidates with the desired affinity from a pool of thousands of antibody clones remains a challenge. Here, we describe a high-throughput procedure that allows reliable affinity screening of unpurified immunoglobulin G or antibody fragments. The method is based on the principle of solution equilibrium titration (SET) using highly sensitive electrochemiluminescence as a readout system. Because the binding partners are not labeled, the resulting KD represents a sound approximation of the real affinity. For screening, diluted bacterial lysates or cell culture supernatants are equilibrated with four different concentrations of a soluble target molecule, and unbound antibodies are subsequently quantified on 384-well Meso Scale Discovery (MSD) plates coated with the respective antigen. For determination of KD values from the resulting titration curves, fit models deduced from the law of mass action for 1:1 and 2:1 binding modes are applied to assess hundreds of interactions simultaneously. The accuracy of the method is demonstrated by comparing results from different screening campaigns from affinity optimization projects with results from detailed affinity characterization.
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