1
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Schueder F, Rivera-Molina F, Su M, Marin Z, Kidd P, Rothman JE, Toomre D, Bewersdorf J. Unraveling cellular complexity with transient adapters in highly multiplexed super-resolution imaging. Cell 2024; 187:1769-1784.e18. [PMID: 38552613 DOI: 10.1016/j.cell.2024.02.033] [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: 05/17/2023] [Revised: 12/22/2023] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Mapping the intricate spatial relationships between the many different molecules inside a cell is essential to understanding cellular functions in all their complexity. Super-resolution fluorescence microscopy offers the required spatial resolution but struggles to reveal more than four different targets simultaneously. Exchanging labels in subsequent imaging rounds for multiplexed imaging extends this number but is limited by its low throughput. Here, we present a method for rapid multiplexed super-resolution microscopy that can, in principle, be applied to a nearly unlimited number of molecular targets by leveraging fluorogenic labeling in conjunction with transient adapter-mediated switching for high-throughput DNA-PAINT (FLASH-PAINT). We demonstrate the versatility of FLASH-PAINT with four applications: mapping nine proteins in a single mammalian cell, elucidating the functional organization of primary cilia by nine-target imaging, revealing the changes in proximity of thirteen different targets in unperturbed and dissociated Golgi stacks, and investigating and quantifying inter-organelle contacts at 3D super-resolution.
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Affiliation(s)
- Florian Schueder
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
| | | | - Maohan Su
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Zach Marin
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Phylicia Kidd
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - James E Rothman
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Derek Toomre
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Nanobiology Institute, Yale University, West Haven, CT, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA; Department of Physics, Yale University, New Haven, CT, USA.
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2
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van Aalen EA, Lurvink JJJ, Vermeulen L, van Gerven B, Ni Y, Arts R, Merkx M. Turning Antibodies into Ratiometric Bioluminescent Sensors for Competition-Based Homogeneous Immunoassays. ACS Sens 2024; 9:1401-1409. [PMID: 38380622 PMCID: PMC10964239 DOI: 10.1021/acssensors.3c02478] [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: 11/20/2023] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/22/2024]
Abstract
Here we present LUCOS (Luminescent Competition Sensor), a modular and broadly applicable bioluminescent diagnostic platform enabling the detection of both small molecules and protein biomarkers. The construction of LUCOS sensors entails the covalent and site-specific coupling of a bioluminescent sensor component to an analyte-specific antibody via protein G-mediated photoconjugation. Target detection is accomplished through intramolecular competition with a tethered analyte competitor for antibody binding. We established two variants of LUCOS: an inherent ratiometric LUCOSR variant and an intensiometric LUCOSI version, which can be used for ratiometric detection upon the addition of a split calibrator luciferase. To demonstrate the versatility of the LUCOS platform, sensors were developed for the detection of the small molecule cortisol and the protein biomarker NT-proBNP. Sensors for both targets displayed analyte-dependent changes in the emission ratio and enabled detection in the micromolar concentration range (KD,app = 16-92 μM). Furthermore, we showed that the response range of the LUCOS sensor can be adjusted by attenuating the affinity of the tethered NT-proBNP competitor, which enabled detection in the nanomolar concentration range (KD,app = 317 ± 26 nM). Overall, the LUCOS platform offers a highly versatile and easy method to convert commercially available monoclonal antibodies into bioluminescent biosensors that provide a homogeneous alternative for the competitive immunoassay.
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Affiliation(s)
- Eva A. van Aalen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Joep J. J. Lurvink
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Leandra Vermeulen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Benice van Gerven
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Yan Ni
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Remco Arts
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, Eindhoven 5600 MB, The
Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
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3
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Chan A, Tsourkas A. Intracellular Protein Delivery: Approaches, Challenges, and Clinical Applications. BME FRONTIERS 2024; 5:0035. [PMID: 38282957 PMCID: PMC10809898 DOI: 10.34133/bmef.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024] Open
Abstract
Protein biologics are powerful therapeutic agents with diverse inhibitory and enzymatic functions. However, their clinical use has been limited to extracellular applications due to their inability to cross plasma membranes. Overcoming this physiological barrier would unlock the potential of protein drugs for the treatment of many intractable diseases. In this review, we highlight progress made toward achieving cytosolic delivery of recombinant proteins. We start by first considering intracellular protein delivery as a drug modality compared to existing Food and Drug Administration-approved drug modalities. Then, we summarize strategies that have been reported to achieve protein internalization. These techniques can be broadly classified into 3 categories: physical methods, direct protein engineering, and nanocarrier-mediated delivery. Finally, we highlight existing challenges for cytosolic protein delivery and offer an outlook for future advances.
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Affiliation(s)
| | - Andrew Tsourkas
- Department of Bioengineering,
University of Pennsylvania, Philadelphia, PA, USA
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4
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Biewenga L, Vermathen R, Rosier BJ, Merkx M. A Generic Antibody-Blocking Protein That Enables pH-Switchable Activation of Antibody Activity. ACS Chem Biol 2024; 19:48-57. [PMID: 38110237 PMCID: PMC10804362 DOI: 10.1021/acschembio.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023]
Abstract
Molecular strategies that allow for reversible control of antibody activity have drawn considerable interest for both therapeutic and diagnostic applications. Protein M is a generic antibody-binding protein that binds to the Fv domain of IgGs and, in doing so, blocks antigen binding. However, the dissociation of protein M is essentially irreversible, which has precluded its use as an antibody affinity reagent and molecular mask to control antibody activity. Here, we show that introduction of 8 histidine residues on the Fv binding interface of protein M results in a variant that shows pH-switchable IgG binding. This protein M-8his variant provides an attractive and universal affinity resin for the purification of IgGs, antibody fragments (Fab and single-chain variable fragments (scFv)), and antibody conjugates. Moreover, protein M-8his enables the pH-dependent blocking of therapeutic antibodies, allowing the selective targeting of cells at pH 6.0.
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Affiliation(s)
- Lieuwe Biewenga
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Robin Vermathen
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Bas J.H.M. Rosier
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
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5
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Rao M, Murali S, Amores D, Yu F, Tsourkas A. Exploring the Sensitivity of Antibody-Drug Conjugate Efficacy to the Selection of Payload, Antibody, and Cell line. Bioconjug Chem 2024; 35:115-124. [PMID: 38173338 PMCID: PMC10872414 DOI: 10.1021/acs.bioconjchem.3c00537] [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] [Indexed: 01/05/2024]
Abstract
Antibody-drug conjugates (ADCs) make up a growing class of targeted therapeutics with important applications in cancer treatment. ADCs are highly modular in nature and thus can be engineered to target any cancer type, but their efficacy is strongly influenced by the specific choice of payload, antibody, and target cell. Considering the number of possible antibody-payload combinations, ADC development would benefit from an efficient method to narrow the number of ADC compositions to those with the highest and most universal potency prior to assessing pharmacokinetics and pharmacodynamics in animal models. To facilitate the identification of optimal ADC compositions, we describe the use of photoreactive antibody-binding domain-drug conjugates (known commercially as oYo-Link) to enable the site-specific labeling of off-the-shelf antibodies. This approach allows for the rapid generation of ADCs with a drug-to-antibody ratio of ∼2 with no subsequent purification required. As a demonstration of this approach, ADCs were generated with different combinations of tubulin-inhibitor drugs (DM1, DM4, VcMMAE, and VcMMAF) and anti-EGFR antibodies (cetuximab, panitumumab, anti-EGFR clone 425, and anti-EGFR clone 528) and were delivered to three EGFR-expressing cell lines (A431, A549, and MDA-MB-231). Real-time cytolysis assays indicated that the most effective antibody varied based on the choice of cell line: cetuximab was most potent against A431 cells, while 425 and 528 led to the greatest cytotoxicity against A549 and MDA-MB-231 cells. These results did not correlate with differences in measured anti-EGFR binding affinity as cetuximab had the highest affinity across all three cell lines, while 425 and 528 had the lowest affinities for all three cell lines. Panitumumab, which had the second-highest anti-EGFR affinity, exhibited the least effective cytolysis across A431, A549, and MDA-MB-231 cells. By demonstrating that ADC potency toward a given target is dependent on both the antibody and drug chosen, these findings can guide the selection of ADCs for further in vivo analysis.
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Affiliation(s)
- Mara Rao
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 USA
| | - Shruthi Murali
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 USA
| | | | - Feifan Yu
- AlphaThera, Inc, Philadelphia, Pennsylvania, 19146 USA
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104 USA
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6
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Kim S, Kim S, Kim S, Kim N, Lee SW, Yi H, Lee S, Sim T, Kwon Y, Lee HS. Affinity-Directed Site-Specific Protein Labeling and Its Application to Antibody-Drug Conjugates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306401. [PMID: 38032124 PMCID: PMC10811483 DOI: 10.1002/advs.202306401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Indexed: 12/01/2023]
Abstract
Chemically modified proteins have diverse applications; however, conventional chemo-selective methods often yield heterogeneously labeled products. To address this limitation, site-specific protein labeling holds significant potential, driving extensive research in this area. Nevertheless, site-specific modification of native proteins remains challenging owing to the complexity of their functional groups. Therefore, a method for site-selective labeling of intact proteins is aimed to design. In this study, a novel approach to traceless affinity-directed intact protein labeling is established, which leverages small binding proteins and genetic code expansion technology. By applying this method, a site-specific antibody labeling with a drug, which leads to the production of highly effective antibody-drug conjugates specifically targeting breast cancer cell lines is achieved. This approach enables traceless conjugation of intact target proteins, which is a critical advantage in pharmaceutical applications. Furthermore, small helical binding proteins can be easily engineered for various target proteins, thereby expanding their potential applications in diverse fields. This innovative approach represents a significant advancement in site-specific modification of native proteins, including antibodies. It also bears immense potential for facilitating the development of therapeutic agents for various diseases.
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Affiliation(s)
- Sooin Kim
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Sanggil Kim
- New Drug Development CenterOsong Medical Innovation Foundation123 Osongsaengmyeong‐ro, Heungdeok‐guCheongjuChungbuk28160Republic of Korea
| | - Sangji Kim
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Namkyoung Kim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Sang Won Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Hanbin Yi
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Seungeun Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Taebo Sim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Yongseok Kwon
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Hyun Soo Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
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7
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Matsuura K, Inaba H. Photoresponsive peptide materials: Spatiotemporal control of self-assembly and biological functions. BIOPHYSICS REVIEWS 2023; 4:041303. [PMID: 38505425 PMCID: PMC10903425 DOI: 10.1063/5.0179171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/27/2023] [Indexed: 03/21/2024]
Abstract
Peptides work as both functional molecules to modulate various biological phenomena and self-assembling artificial materials. The introduction of photoresponsive units to peptides allows the spatiotemporal remote control of their structure and function upon light irradiation. This article overviews the photoresponsive peptide design, interaction with biomolecules, and applications in self-assembling materials over the last 30 years. Peptides modified with photochromic (photoisomerizable) molecules, such as azobenzene and spiropyran, reversibly photo-controlled the binding to biomolecules and nanostructure formation through self-assembly. Photocleavable molecular units irreversibly control the functions of peptides through cleavage of the main chain and deprotection by light. Photocrosslinking between peptides or between peptides and other biomolecules enhances the structural stability of peptide assemblies and complexes. These photoresponsive peptides spatiotemporally controlled the formation and dissociation of peptide assemblies, gene expressions, protein-drug interactions, protein-protein interactions, liposome deformation and motility, cytoskeleton structure and stability, and cell functions by appropriate light irradiation. These molecular systems can be applied to photo-control biological functions, molecular robots, artificial cells, and next-generation smart drug delivery materials.
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8
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Moerman PG, Fang H, Videbæk TE, Rogers WB, Schulman R. A simple method to alter the binding specificity of DNA-coated colloids that crystallize. SOFT MATTER 2023; 19:8779-8789. [PMID: 37942543 DOI: 10.1039/d3sm01105d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond, opening avenues to producing structures with useful photonic properties. The potential design space of DNA-coated colloids is large, but its exploration is hampered by a reliance on chemically modified DNA that is slow and expensive to commercially synthesize. Here we introduce a method to controllably tailor the sequences of DNA-coated particles by covalently appending new sequence domains onto the DNA grafted to colloidal particles. The tailored particles crystallize as readily and at the same temperature as those produced via direct chemical synthesis, making them suitable for self-assembly. Moreover, we show that particles coated with a single sequence can be converted into a variety of building blocks with differing specificities by appending different DNA sequences to them. This method will make it practical to identify optimal and complex particle sequence designs and paves the way to programming the assembly kinetics of DNA-coated colloids.
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Affiliation(s)
- Pepijn G Moerman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, 5612 AE Eindhoven, The Netherlands
| | - Huang Fang
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China
| | - Thomas E Videbæk
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
| | - W Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA 02453, USA.
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
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9
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van Aalen EA, de Vries IR, Hanckmann ETL, Stevens JRF, Romagnoli TR, Derijks LJJ, Broeren MAC, Merkx M. Point-of-care therapeutic drug monitoring of tumour necrosis factor-α inhibitors using a single step immunoassay. SENSORS & DIAGNOSTICS 2023; 2:1492-1500. [PMID: 38013761 PMCID: PMC10633107 DOI: 10.1039/d3sd00131h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/04/2023] [Indexed: 11/29/2023]
Abstract
Therapeutic drug monitoring (TDM) of tumor necrosis factor-α (TNFα)-inhibitors adalimumab and infliximab is important to establish optimal drug dose and maximize treatment efficacy. Currently, TDM is primarily performed with ELISA techniques in clinical laboratories, resulting in a long sample-to-result workflow. Point-of-care (POC) detection of these therapeutic antibodies could significantly decrease turnaround times and allow for user-friendly home-testing. Here, we adapted the recently developed bioluminescent dRAPPID (dimeric Ratiometric Plug-and-Play Immunodiagnostics) sensor platform to allow POC TDM of infliximab and adalimumab. We applied the two best performing dRAPPID sensors, with limit-of-detections of 1 pM and 17 pM, to measure the infliximab and adalimumab levels in 49 and 40 patient serum samples, respectively. The analytical performance of dRAPPID was benchmarked with commercial ELISAs and yielded Pearson's correlation coefficients of 0.93 and 0.94 for infliximab and adalimumab, respectively. Furthermore, a dedicated bioluminescence reader was fabricated and used as a readout device for the TDM dRAPPID sensors. Subsequently, infliximab and adalimumab patient serum samples were measured with the TDM dRAPPID sensors and bioluminescence reader, yielding Pearson's correlation coefficients of 0.97 and 0.86 for infliximab and adalimumab, respectively, and small proportional differences with ELISA (slope was 0.97 ± 0.09 and 0.96 ± 0.20, respectively). The adalimumab and infliximab dRAPPID sensors, in combination with the dedicated bioluminescence reader, allow for ease-of-use TDM with a fast turnaround time and show potential for POC TDM outside of clinical laboratories.
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Affiliation(s)
- Eva A van Aalen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Ivar R de Vries
- Department of Electrical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Eva T L Hanckmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Jeannot R F Stevens
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Thomas R Romagnoli
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Luc J J Derijks
- Department of Clinical Pharmacy and Pharmacology, Máxima Medical Center P.O. Box 7777 5500 MB Veldhoven The Netherlands
- Department of Clinical Pharmacy and Toxicology, Maastricht University Medical Center P.O. Box 5800 6202 AZ Maastricht The Netherlands
| | - Maarten A C Broeren
- Laboratory of Clinical Chemistry and Haematology, Máxima Medical Center P.O. Box 7777 5500 MB Veldhoven The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands +31 40 247 4728
- Institute for Complex Molecular Systems, Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
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10
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Pakula RJ, Scott PJH. Applications of radiolabeled antibodies in neuroscience and neuro-oncology. J Labelled Comp Radiopharm 2023; 66:269-285. [PMID: 37322805 DOI: 10.1002/jlcr.4049] [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: 03/04/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
Positron emission tomography (PET) is a powerful tool in medicine and drug development, allowing for non-invasive imaging and quantitation of biological processes in live organisms. Targets are often probed with small molecules, but antibody-based PET is expanding because of many benefits, including ease of design of new antibodies toward targets, as well as the very strong affinities that can be expected. Application of antibodies to PET imaging of targets in the central nervous system (CNS) is a particularly nascent field, but one with tremendous potential. In this review, we discuss the growth of PET in imaging of CNS targets, present the promises and progress in antibody-based CNS PET, explore challenges faced by the field, and discuss questions that this promising approach will need to answer moving forward for imaging and perhaps even radiotherapy.
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Affiliation(s)
- Ryan J Pakula
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter J H Scott
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
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11
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Niu J, Hagen J, Yu F, Kalyuzhny AE, Tsourkas A. Labeling of Phospho-Specific Antibodies with oYo-Link® Epitope Tags for Multiplex Immunostaining. Methods Mol Biol 2023; 2593:113-126. [PMID: 36513927 PMCID: PMC10730302 DOI: 10.1007/978-1-0716-2811-9_7] [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] [Indexed: 12/15/2022]
Abstract
Spatial proteomics has recently garnered significant interest, as it offers to provide unprecedented insight into biological processes in both health and disease, by connecting protein expression patterns from the subcellular level to the tissue or even organism level. These high-content approaches generally rely on a high degree of multiplexing, whereby multiple proteins can be detected simultaneously. The most versatile multiplexing approaches utilize antibodies to confer specificity for various intracellular proteins of interest. Therefore, these methods must be able to differentiate many antibodies at once. In this chapter, we describe a simple and rapid approach to labeling antibodies with distinct epitope tags in a site-specific manner. This allows multiple antibodies, even from the same host species, to be uniquely identified and detected and offers a simple approach for spatial proteomic applications.
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Affiliation(s)
| | | | | | | | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Brasino M, Wagnell E, Hamilton S, Ranganathan S, Gomes MM, Branchaud B, Messmer B, Ibsen SD. Turning antibodies off and on again using a covalently tethered blocking peptide. Commun Biol 2022; 5:1357. [PMID: 36496512 PMCID: PMC9741643 DOI: 10.1038/s42003-022-04094-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022] Open
Abstract
In their natural form, antibodies are always in an "on-state" and are capable of binding to their targets. This leads to undesirable interactions in a wide range of therapeutic, analytical, and synthetic applications. Modulating binding kinetics of antibodies to turn them from an "off-state" to an "on-state" with temporal and spatial control can address this. Here we demonstrate a method to modulate binding activity of antibodies in a predictable and reproducible way. We designed a blocking construct that uses both covalent and non-covalent interactions with the antibody. The construct consisted of a Protein L protein attached to a flexible linker ending in a blocking-peptide designed to interact with the antibody binding site. A mutant Protein L was developed to enable photo-triggered covalent crosslinking to the antibody at a specific location. The covalent bond anchored the linker and blocking peptide to the antibody light chain keeping the blocking peptide close to the antibody binding site. This effectively put the antibody into an "off-state". We demonstrate that protease-cleavable and photocleavable moieties in the tether enable controlled antibody activation to the "on-state" for anti-FLAG and cetuximab antibodies. Protein L can bind a range of antibodies used therapeutically and in research for wide applicability.
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Affiliation(s)
- Michael Brasino
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | - Eli Wagnell
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | - Sean Hamilton
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97201 USA
| | - Srivathsan Ranganathan
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | - Michelle M. Gomes
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | - Bruce Branchaud
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA
| | | | - Stuart D. Ibsen
- grid.5288.70000 0000 9758 5690Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201 USA ,grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, School of Medicine, Oregon Health and Science University, Portland, OR 97201 USA
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13
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Watson EE, Winssinger N. Synthesis of Protein-Oligonucleotide Conjugates. Biomolecules 2022; 12:biom12101523. [PMID: 36291732 PMCID: PMC9599799 DOI: 10.3390/biom12101523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Nucleic acids and proteins form two of the key classes of functional biomolecules. Through the ability to access specific protein-oligonucleotide conjugates, a broader range of functional molecules becomes accessible which leverages both the programmability and recognition potential of nucleic acids and the structural, chemical and functional diversity of proteins. Herein, we summarize the available conjugation strategies to access such chimeric molecules and highlight some key case study examples within the field to showcase the power and utility of such technology.
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Affiliation(s)
- Emma E. Watson
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (E.E.W.); (N.W.)
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, CH-1205 Geneva, Switzerland
- Correspondence: (E.E.W.); (N.W.)
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14
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Efficient DNA fluorescence labeling via base excision trapping. Nat Commun 2022; 13:5043. [PMID: 36028479 PMCID: PMC9418136 DOI: 10.1038/s41467-022-32494-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/03/2022] [Indexed: 01/19/2023] Open
Abstract
Fluorescence labeling of DNAs is broadly useful, but methods for labeling are expensive and labor-intensive. Here we describe a general method for fluorescence labeling of oligonucleotides readily and cost-efficiently via base excision trapping (BETr), employing deaminated DNA bases to mark label positions, which are excised by base excision repair enzymes generating AP sites. Specially designed aminooxy-substituted rotor dyes trap the AP sites, yielding high emission intensities. BETr is orthogonal to DNA synthesis by polymerases, enabling multi-uracil incorporation into an amplicon and in situ BETr labeling without washing. BETr also enables labeling of dsDNA such as genomic DNA at a high labeling density in a single tube by use of nick translation. Use of two different deaminated bases facilitates two-color site-specific labeling. Use of a multi-labeled DNA construct as a bright fluorescence tag is demonstrated through the conjugation to an antibody for imaging proteins. Finally, double-strand selectivity of a repair enzyme is harnessed in sensitive reporting on the presence of a target DNA or RNA in a mixture with isothermal turnover and single nucleotide specificity. Overall, the results document a convenient and versatile method for general fluorescence labeling of DNAs.
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15
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McCue AC, Yao Z, Kuhlman B. Advances in modular control of CAR-T therapy with adapter-mediated CARs. Adv Drug Deliv Rev 2022; 187:114358. [PMID: 35618140 PMCID: PMC9939278 DOI: 10.1016/j.addr.2022.114358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/01/2022]
Abstract
Protein engineering has contributed to successes in the field of T cell-based immunotherapy, including chimeric antigen receptor (CAR) T cell therapy. CAR T cell therapy has become a pillar of cancer immunotherapy, demonstrating clinical effectiveness against B cell malignancies by targeting the B cell antigen CD19. Current gene editing techniques have limited safety controls over CAR T cell activity, which presents a hurdle for control of CAR T cells in patients. Alternatively, CAR T cell activity can be controlled by engineering CARs to bind soluble adapter molecules that direct the interaction between the CAR T cell and target cell. The flexibility in this adapter-mediated approach overcomes the rigid specificity of traditional CAR T cells to allow targeting of multiple cell types. Here we describe adapter CAR T technologies and how these methods emphasize the growing role of protein engineering in the design of programmable tools for T cell therapies.
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Affiliation(s)
- Amelia C McCue
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Zhiyuan Yao
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27514, USA.
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16
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Jeon CH, Ha TH. Covalent and Oriented Immobilization of Antibodies through Systematic Modification of Photoactivatable RNA Hybrid Aptamers. Bioconjug Chem 2022; 33:1527-1535. [DOI: 10.1021/acs.bioconjchem.2c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chang Hoon Jeon
- Core Research Facility & Analysis Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Tai Hwan Ha
- Core Research Facility & Analysis Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, South Korea
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17
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Zappala F, Higbee-Dempsey E, Jang B, Miller J, Yan L, Minutolo NG, Rosado González GT, Tsourkas A, Ozdemir BA. Rapid, site-specific labeling of "off-the-shelf" and native serum autoantibodies with T cell-redirecting domains. SCIENCE ADVANCES 2022; 8:eabn4613. [PMID: 35522741 PMCID: PMC9075798 DOI: 10.1126/sciadv.abn4613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
Extensive antibody engineering and cloning is typically required to generate new bispecific antibodies. Made-to-order genes, advanced expression systems, and high-efficiency cloning can simplify and accelerate this process, but it still can take months before a functional product is realized. We developed a simple method to site-specifically and covalently attach a T cell-redirecting domain to any off-the-shelf, human immunoglobulin G (IgG) or native IgG isolated from serum. No antibody engineering, cloning, or knowledge of the antibody sequence is required. Bispecific antibodies are generated in just hours. By labeling antibodies isolated from tumor-bearing mice, including two syngeneic models, we generated T cell-redirecting autoantibodies (TRAAbs) that act as an effective therapeutic. TRAAbs preferentially bind tumor tissue over healthy tissue, indicating a previously unexplored therapeutic window. The use of autoantibodies to direct the tumor targeting of bispecific antibodies represents a new paradigm in personalized medicine that eliminates the need to identify tumor biomarkers.
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Affiliation(s)
- Fabiana Zappala
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Elizabeth Higbee-Dempsey
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Bian Jang
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Joann Miller
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Lesan Yan
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Nicholas G. Minutolo
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA
| | - Gabriela T. Rosado González
- Gabriela T. Rosado González, Department of Chemistry, University of Puerto Rico, 14, 2534 Av. Universidad Ste. 1401, San Juan, 00925 Puerto Rico
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Burcin Altun Ozdemir
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
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18
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van Aalen EA, Wouters SFA, Verzijl D, Merkx M. Bioluminescent RAPPID Sensors for the Single-Step Detection of Soluble Axl and Multiplex Analysis of Cell Surface Cancer Biomarkers. Anal Chem 2022; 94:6548-6556. [PMID: 35438976 PMCID: PMC9069438 DOI: 10.1021/acs.analchem.2c00297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Early diagnosis of
cancer is essential for the efficacy of treatment.
Our group recently developed RAPPID, a bioluminescent immunoassay
platform capable of measuring a wide panel of biomarkers directly
in solution. Here, we developed and systematically screened different
RAPPID sensors for sensitive detection of the soluble fraction of
Axl (sAxl), a cell surface receptor that is overexpressed in several
types of cancer. The best-performing RAPPID sensor, with a limit of
detection of 8 pM and a >9-fold maximal change in
emission
ratio, was applied to measure Axl in three different contexts: clinically
relevant sAxl levels (∼0.5 and ∼1 nM) in diluted blood
plasma, proteolytically cleaved Axl in the cell culture medium of
A431 and HeLa cancer cells, and Axl on the membrane of A431 cells.
We further extended the sensor toolbox by developing dual-color RAPPID
for simultaneous detection of Axl and EGFR on A431 and HeLa cells,
as well as an AND-gate RAPPID that measures the concurrent presence
of these two cell surface receptors on the same cell. These new RAPPID
sensors provide attractive alternatives for more laborious protein
detection and quantification methods such as FACS and immunostainings,
due to their simple practical implantation and low intrinsic background
signal.
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Affiliation(s)
- Eva A van Aalen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | - Simone F A Wouters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
| | | | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O Box 513, 5600 MB Eindhoven, The Netherlands
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19
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Earley D, Guillou A, Klingler S, Fay R, Gut M, d’Orchymont F, Behmaneshfar S, Reichert L, Holland JP. Charting the Chemical and Mechanistic Scope of Light-Triggered Protein Ligation. JACS AU 2022; 2:646-664. [PMID: 35373206 PMCID: PMC8970001 DOI: 10.1021/jacsau.1c00530] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Indexed: 05/04/2023]
Abstract
The creation of discrete, covalent bonds between a protein and a functional molecule like a drug, fluorophore, or radiolabeled complex is essential for making state-of-the-art tools that find applications in basic science and clinical medicine. Photochemistry offers a unique set of reactive groups that hold potential for the synthesis of protein conjugates. Previous studies have demonstrated that photoactivatable desferrioxamine B (DFO) derivatives featuring a para-substituted aryl azide (ArN3) can be used to produce viable zirconium-89-radiolabeled monoclonal antibodies (89Zr-mAbs) for applications in noninvasive diagnostic positron emission tomography (PET) imaging of cancers. Here, we report on the synthesis, 89Zr-radiochemistry, and light-triggered photoradiosynthesis of 89Zr-labeled human serum albumin (HSA) using a series of 14 different photoactivatable DFO derivatives. The photoactive groups explore a range of substituted, and isomeric ArN3 reagents, as well as derivatives of benzophenone, a para-substituted trifluoromethyl phenyl diazirine, and a tetrazole species. For the compounds studied, efficient photochemical activation occurs inside the UVA-to-visible region of the electromagnetic spectrum (∼365-450 nm) and the photochemical reactions with HSA in water were complete within 15 min under ambient conditions. Under standardized experimental conditions, photoradiosynthesis with compounds 1-14 produced the corresponding 89ZrDFO-PEG3-HSA conjugates with decay-corrected isolated radiochemical yields between 18.1 ± 1.8% and 62.3 ± 3.6%. Extensive density functional theory (DFT) calculations were used to explore the reaction mechanisms and chemoselectivity of the light-induced bimolecular conjugation of compounds 1-14 to protein. The photoactivatable DFO-derivatives operate by at least five distinct mechanisms, each producing a different type of bioconjugate bond. Overall, the experimental and computational work presented here confirms that photochemistry is a viable option for making diverse, functionalized protein conjugates.
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20
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Adak AK, Huang KT, Liao CY, Lee YJ, Kuo WH, Huo YR, Li PJ, Chen YJ, Chen BS, Chen YJ, Chu Hwang K, Wayne Chang WS, Lin CC. Investigating a Boronate-Affinity-Guided Acylation Reaction for Labelling Native Antibodies. Chemistry 2022; 28:e202104178. [PMID: 35143090 DOI: 10.1002/chem.202104178] [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: 11/20/2021] [Indexed: 12/12/2022]
Abstract
The excellent molecular recognition capabilities of monoclonal antibodies (mAbs) have opened up exciting opportunities for biotherapeutic discovery. Taking advantage of the full potential of this tool necessitates affinity ligands capable of conjugating directly with small molecules to a defined degree of biorthogonality, especially when modifying natural Abs. Herein, a bioorthogonal boronate-affinity-based Ab ligand featuring a 4-(dimethylamino)pyridine and an S-aryl thioester to label full-length Abs is reported. The photoactivatable linker in the acyl donor facilitated purification of azide-labelled Ab (N3 -Ab) was quantitatively cleaved upon brief exposure to UV light while retaining the original Ab activity. Click reactions enabled the precise addition of biotin, a fluorophore, and a pharmacological agent to the purified N3 -Abs. The resulting immunoconjugate showed selectivity against targeted cells. Bioorthogonal traceless design and reagentless purification allow this strategy to be a powerful tool to engineer native antibodies amenable to therapeutic intervention.
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Affiliation(s)
- Avijit K Adak
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Kuan-Ting Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Chien-Yu Liao
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, 350, Taiwan
| | - Yuan-Jung Lee
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wen-Hua Kuo
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yi-Ren Huo
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Pei-Jhen Li
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Bo-Shiun Chen
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Kuo Chu Hwang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Wun-Shang Wayne Chang
- National Institute of Cancer Research, National Health Research Institutes, Miaoli, 350, Taiwan
| | - Chun-Cheng Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu, 300, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
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21
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22
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Mei L, Zappala F, Tsourkas A. Rapid Production of Bispecific Antibodies from Off-the-Shelf IgGs with High Yield and Purity. Bioconjug Chem 2022; 33:134-141. [PMID: 34894663 PMCID: PMC9104846 DOI: 10.1021/acs.bioconjchem.1c00476] [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: 01/21/2023]
Abstract
Bispecific antibodies (BsAb) refer to a class of biomacromolecules that are capable of binding two antigens or epitopes simultaneously. This can elicit unique biological effects that cannot be achieved with either individual antibody or two unlinked antibodies. Bispecific antibodies have been used for targeting effector cells to tumor cells, preferential targeting of cells expressing two target biomarkers over cells expressing either target biomarker individually, or to couple two molecular targets on the same cell surface to trigger unique intracellular signaling pathways. Here, we present two related methods that enable direct, rapid assembly of bispecific antibodies from any two "off-the-shelf" Immunoglobulin G (IgG) antibodies, in as little as 1 day. Both workflows can be summarized into two steps: (1) attach a small photoreactive antibody binding domain (pAbBD) fused to SpyCatcher or SpyTag (peptide-protein partners derived from the S. pyogenes fibronectin-binding protein FbaB) to each component IgG, respectively; (2) assemble the BsAb through the spontaneous isopeptide bond formation that occurs between SpyTag and SpyCatcher. These approaches enable production of BsAbs from any two IgG molecules without the need to elucidate their amino acid sequences or genetically alter their structure. Binding assays and T cell-mediated cytolysis assays were performed to validate the binding and functional properties of Trastuzumab × Cetuximab BsAb and Cetuximab × OKT3 BsAb, respectively. This approach enables rapid, low-cost production of highly homogeneous tetravalent BsAbs in a modular fashion, presenting an opportunity to quickly evaluate antibody pairs in a BsAb format for unique or synergistic functionalities.
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Affiliation(s)
- Linghan Mei
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Fabiana Zappala
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104,Corresponding author:, Phone: 215-898-8167, Address: Andrew Tsourkas, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33rd Street, Philadelphia, PA 19104 USA
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23
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Seitz I, Shaukat A, Nurmi K, Ijäs H, Hirvonen J, Santos HA, Kostiainen MA, Linko V. Prospective Cancer Therapies Using Stimuli-Responsive DNA Nanostructures. Macromol Biosci 2021; 21:e2100272. [PMID: 34614301 DOI: 10.1002/mabi.202100272] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/28/2021] [Indexed: 11/08/2022]
Abstract
Nanostructures based on DNA self-assembly present an innovative way to address the increasing need for target-specific delivery of therapeutic molecules. Currently, most of the chemotherapeutics being used in clinical practice have undesired and exceedingly high off-target toxicity. This is a challenge in particular for small molecules, and hence, developing robust and effective methods to lower these side effects and enhance the antitumor activity is of paramount importance. Prospectively, these issues could be tackled with the help of DNA nanotechnology, which provides a route for the fabrication of custom, biocompatible, and multimodal structures, which can, to some extent, resist nuclease degradation and survive in the cellular environment. Similar to widely employed liposomal products, the DNA nanostructures (DNs) are loaded with selected drugs, and then by employing a specific stimulus, the payload can be released at its target region. This review explores several strategies and triggers to achieve targeted delivery of DNs. Notably, different modalities are explained through which DNs can interact with their respective targets as well as how structural changes triggered by external stimuli can be used to achieve the display or release of the cargo. Furthermore, the prospects and challenges of this technology are highlighted.
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Affiliation(s)
- Iris Seitz
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Ahmed Shaukat
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Kurt Nurmi
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, 00014, Finland
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland.,Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, 40014, Finland
| | - Jouni Hirvonen
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, 00014, Finland
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, 00014, Finland.,Department of Biomedical Engineering, W.J. Kolff Institute for Biomedical Engineering and Materials Science, University of Groningen, University Medical Center Groningen, Ant. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland.,HYBER Centre, Department of Applied Physics, Aalto University, P.O. Box 15100, Aalto, 00076, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland.,HYBER Centre, Department of Applied Physics, Aalto University, P.O. Box 15100, Aalto, 00076, Finland
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24
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von Witting E, Hober S, Kanje S. Affinity-Based Methods for Site-Specific Conjugation of Antibodies. Bioconjug Chem 2021; 32:1515-1524. [PMID: 34369763 PMCID: PMC8377709 DOI: 10.1021/acs.bioconjchem.1c00313] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conjugation of various reagents to antibodies has long been an elegant way to combine the superior binding features of the antibody with other desired but non-natural functions. Applications range from labels for detection in different analytical assays to the creation of new drugs by conjugation to molecules which improves the pharmaceutical effect. In many of these applications, it has been proven advantageous to control both the site and the stoichiometry of the conjugation to achieve a homogeneous product with predictable, and often also improved, characteristics. For this purpose, many research groups have, during the latest decade, reported novel methods and techniques, based on small molecules, peptides, and proteins with inherent affinity for the antibody, for site-specific conjugation of antibodies. This review provides a comprehensive overview of these methods and their applications and also describes a historical perspective of the field.
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Affiliation(s)
- Emma von Witting
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Centre, SE-114 19, Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Centre, SE-114 19, Stockholm, Sweden
| | - Sara Kanje
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Centre, SE-114 19, Stockholm, Sweden
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25
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A plug-and-play platform of ratiometric bioluminescent sensors for homogeneous immunoassays. Nat Commun 2021; 12:4586. [PMID: 34321486 PMCID: PMC8319308 DOI: 10.1038/s41467-021-24874-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 07/08/2021] [Indexed: 01/07/2023] Open
Abstract
Heterogeneous immunoassays such as ELISA have become indispensable in modern bioanalysis, yet translation into point-of-care assays is hindered by their dependence on external calibration and multiple washing and incubation steps. Here, we introduce RAPPID (Ratiometric Plug-and-Play Immunodiagnostics), a mix-and-measure homogeneous immunoassay platform that combines highly specific antibody-based detection with a ratiometric bioluminescent readout. The concept entails analyte-induced complementation of split NanoLuc luciferase fragments, photoconjugated to an antibody sandwich pair via protein G adapters. Introduction of a calibrator luciferase provides a robust ratiometric signal that allows direct in-sample calibration and quantitative measurements in complex media such as blood plasma. We developed RAPPID sensors that allow low-picomolar detection of several protein biomarkers, anti-drug antibodies, therapeutic antibodies, and both SARS-CoV-2 spike protein and anti-SARS-CoV-2 antibodies. With its easy-to-implement standardized workflow, RAPPID provides an attractive, fast, and low-cost alternative to traditional immunoassays, in an academic setting, in clinical laboratories, and for point-of-care applications. Many current immunoassays require multiple washing, incubation and optimization steps. Here the authors present Ratiometric Plug-and-Play Immunodiagnostics (RAPPID), a generic assay platform that uses ratiometric bioluminescent detection to allow sandwich immunoassays to be performed directly in solution.
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26
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Muguruma K, Osawa R, Fukuda A, Ishikawa N, Fujita K, Taguchi A, Takayama K, Taniguchi A, Ito Y, Hayashi Y. Development of a High-Affinity Antibody-Binding Peptide for Site-Specific Modification. ChemMedChem 2021; 16:1813-1820. [PMID: 33594831 DOI: 10.1002/cmdc.202000977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/13/2021] [Indexed: 11/09/2022]
Abstract
Immunoglobulin G (IgG)-binding peptides such as 15-IgBP are convenient tools for the site-specific modification of antibodies and the preparation of homogeneous antibody-drug conjugates. A peptide such as 15-IgBP can be selectively crosslinked to the fragment crystallizable region of human IgG in an affinity-dependent manner via the ϵ-amino group of Lys8. Previously, we found that the peptide 15-Lys8Leu has a high affinity (Kd =8.19 nM) due to the presence of the γ-dimethyl group in Leu8. The primary amino group required for the crosslinking to the antibodies has, however, been lost. Here, we report the design and synthesis of a novel unnatural amino acid, 4-(2-aminoethylcarbamoyl)leucine (Aecl), which possesses both the γ-dimethyl fragment and a primary amino group. A peptide containing Aecl8 (15-Lys8Aecl) was synthesized and showed a binding affinity ten times higher (Kd =24.3 nM) than that of 15-IgBP (Kd =267 nM). Fluorescein isothiocyanate (FITC)-labeled 15-Lys8Aecl with an N-hydroxy succinimide ester at the side chain of Aecl8 (FITC-15-Lys8Aecl(OSu)) successfully labeled an antibody (trastuzumab, Herceptin® ) with the fluorophore. This peptide scaffold has both strong binding affinity and crosslinking capability, and could be a useful tool for the selective chemical modification of antibodies with molecules of interest such as drugs.
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Affiliation(s)
- Kyohei Muguruma
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan.,Present address: Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, 152-8552, Japan
| | - Rento Osawa
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Akane Fukuda
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Naoto Ishikawa
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University Korimoto, Kagoshima, 890-0065, Japan
| | - Konomi Fujita
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Akihiro Taguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Kentaro Takayama
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan.,Present address, Department of Environmental Biochemistry, Kyoto Pharmaceutical University, Kyoto, 607-8414, Japan
| | - Atsuhiko Taniguchi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Yuji Ito
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University Korimoto, Kagoshima, 890-0065, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
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27
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Park J, Lee S, Kim Y, Yoo TH. Methods to generate site-specific conjugates of antibody and protein. Bioorg Med Chem 2021; 30:115946. [DOI: 10.1016/j.bmc.2020.115946] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023]
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28
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Matsuda Y, Mendelsohn BA. An overview of process development for antibody-drug conjugates produced by chemical conjugation technology. Expert Opin Biol Ther 2020; 21:963-975. [PMID: 33141625 DOI: 10.1080/14712598.2021.1846714] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: We discuss chemical conjugation strategies for antibody-drug conjugates (ADCs) from an industrial perspective and compare three promising chemical conjugation technologies to produce site-specific ADCs.Areas covered: Currently, nine ADCs are commercially approved and all are produced by chemical conjugation technology. However, seven of these ADCs contain a relatively broad drug distribution, potentially limiting their therapeutic indices. In 2019, the first site-specific ADC was launched on the market by Daiichi-Sankyo. This achievement, and an analysis of clinical trials over the last decade, indicates that current industrial interest in the ADC field is shifting toward site-specific conjugation technologies. From an industrial point of view, we aim to provide guidance regarding established conjugation methodologies that have already been applied to scale-up stages. With an emphasis on highly productive, scalable, and synthetic process robustness, conjugation methodologies for ADC production is discussed herein.Expert opinion: All three chemical conjugation technologies described in this review have various advantages and disadvantages, therefore drug developers can utilize these depending on their biological and/or protein targets. The future landscape of the ADC field is also discussed.
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Affiliation(s)
- Yutaka Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
| | - Brian A Mendelsohn
- Process Development & Tech Transfer, Ajinomoto Bio-Pharma Services, 11040 Roselle Street, San Diego, CA 92121, United States
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29
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Fc-specific and covalent conjugation of a fluorescent protein to a native antibody through a photoconjugation strategy for fabrication of a novel photostable fluorescent antibody. Anal Bioanal Chem 2020; 413:945-953. [PMID: 33210177 DOI: 10.1007/s00216-020-03051-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 10/22/2022]
Abstract
Fluorophore-antibody conjugates with high photobleaching resistance, high chemical stability, and Fc-specific attachment is a great advantage for immunofluorescence imaging. Here, an Fc-binding protein (Z-domain) carrying a photo-cross-linker (p-benzoylphenylalanine, Bpa) fused with enhanced green fluorescent protein (EGFP), namely photoactivatable ZBpa-EGFP recombinant, was directly generated using the aminoacyl-tRNA synthetase/suppressor tRNA technique without any further modification. By employing the photoactivatable ZBpa-EGFP, an optimal approach was successfully developed which enabled EGFP to site-selectively and covalently attach to native antibody (IgG) with approximately 90% conjugation efficiency. After characterizing the Fc-specific and covalent manner of the EGFP-photoconjugated antibody, its excellent photobleaching resistance for immunofluorescence imaging was demonstrated in a model study by monitoring the toll-like receptor 4 (TLR4) expression in HepG2 cells. The proposed approach here for the preparation of a novel fluorescent antibody is available and reliable, which would play an important role in fluorescence immunoassay, and is expected to be extended to the generation of other biomolecule-photoconjugated antibodies, such as other fluorescent proteins for multiplex immunofluorescence imaging or reporter enzymes for highly sensitive enzyme immunoassays.Graphical abstract.
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30
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Krasitskaya VV, Bashmakova EE, Frank LA. Coelenterazine-Dependent Luciferases as a Powerful Analytical Tool for Research and Biomedical Applications. Int J Mol Sci 2020; 21:E7465. [PMID: 33050422 PMCID: PMC7590018 DOI: 10.3390/ijms21207465] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022] Open
Abstract
: The functioning of bioluminescent systems in most of the known marine organisms is based on the oxidation reaction of the same substrate-coelenterazine (CTZ), catalyzed by luciferase. Despite the diversity in structures and the functioning mechanisms, these enzymes can be united into a common group called CTZ-dependent luciferases. Among these, there are two sharply different types of the system organization-Ca2+-regulated photoproteins and luciferases themselves that function in accordance with the classical enzyme-substrate kinetics. Along with deep and comprehensive fundamental research on these systems, approaches and methods of their practical use as highly sensitive reporters in analytics have been developed. The research aiming at the creation of artificial luciferases and synthetic CTZ analogues with new unique properties has led to the development of new experimental analytical methods based on them. The commercial availability of many ready-to-use assay systems based on CTZ-dependent luciferases is also important when choosing them by first-time-users. The development of analytical methods based on these bioluminescent systems is currently booming. The bioluminescent systems under consideration were successfully applied in various biological research areas, which confirms them to be a powerful analytical tool. In this review, we consider the main directions, results, and achievements in research involving these luciferases.
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Affiliation(s)
- Vasilisa V. Krasitskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Eugenia E. Bashmakova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Ludmila A. Frank
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
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31
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Minutolo NG, Sharma P, Poussin M, Shaw LC, Brown DP, Hollander EE, Smole A, Rodriguez-Garcia A, Hui JZ, Zappala F, Tsourkas A, Powell DJ. Quantitative Control of Gene-Engineered T-Cell Activity through the Covalent Attachment of Targeting Ligands to a Universal Immune Receptor. J Am Chem Soc 2020; 142:6554-6568. [PMID: 32191035 DOI: 10.1021/jacs.9b11622] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Universal immune receptors represent a rapidly emerging form of adoptive T-cell therapy with the potential to overcome safety and antigen escape challenges faced by conventional chimeric antigen receptor (CAR) T-cell therapy. By decoupling antigen recognition and T-cell signaling domains via bifunctional antigen-specific targeting ligands, universal immune receptors can regulate T-cell effector function and target multiple antigens with a single receptor. Here, we describe the development of the SpyCatcher immune receptor, the first universal immune receptor that allows for the post-translational covalent attachment of targeting ligands at the T-cell surface through the application of SpyCatcher-SpyTag chemistry. The SpyCatcher immune receptor redirected primary human T cells against a variety of tumor antigens via the addition of SpyTag-labeled targeting ligands, both in vitro and in vivo. SpyCatcher T-cell activity relied upon the presence of both target antigen and SpyTag-labeled targeting ligand, allowing for dose-dependent control of function. The mutational disruption of covalent bond formation between the receptor and the targeting ligand still permitted redirected T-cell function but significantly compromised antitumor function. Thus, the SpyCatcher immune receptor allows for rapid antigen-specific receptor assembly, multiantigen targeting, and controllable T-cell activity.
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32
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Wouters SA, Vugs WJP, Arts R, de Leeuw NM, Teeuwen RWH, Merkx M. Bioluminescent Antibodies through Photoconjugation of Protein G-Luciferase Fusion Proteins. Bioconjug Chem 2020; 31:656-662. [PMID: 31909607 PMCID: PMC7086395 DOI: 10.1021/acs.bioconjchem.9b00804] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/06/2020] [Indexed: 12/18/2022]
Abstract
Bioluminescent antibodies represent attractive detection agents in both bioanalytical assays and imaging. Currently, their preparation relies on genetic fusion of luciferases to antibodies or nonspecific chemical conjugation strategies. Here, we report a generic method to generate well-defined covalent antibody-luciferase conjugates starting from commercially available monoclonal antibodies. Our approach uses fusion proteins consisting of the bright blue light-emitting luciferase NanoLuc (NL) and an Fc-binding protein domain (Gx) that can be photo-cross-linked to the antibody using UV light illumination. Green and red color variants were constructed by tight fusion of the NanoLuc with a green fluorescent acceptor domain and introduction of Cy3, respectively. To increase the already bright NanoLuc emission, tandem fusions were successfully developed in which the Gx domain is fused to two or three copies of the NanoLuc domain. The Gx-NL fusion proteins can be efficiently photo-cross-linked to all human immunoglobulin G (IgG) isotypes and most mammalian IgG's using 365 nm light, yielding antibodies with either one or two luciferase domains. The bioluminescent antibodies were successfully used in cell immunostaining and bioanalytical assays such as enzyme-linked immunosorbent assay (ELISA) and Western blotting.
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Affiliation(s)
- Simone
F. A. Wouters
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Willem J. P. Vugs
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Remco Arts
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Nynke M. de Leeuw
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Roy W. H. Teeuwen
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and
Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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33
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Gallo E. Fluorogen-Activating Proteins: Next-Generation Fluorescence Probes for Biological Research. Bioconjug Chem 2019; 31:16-27. [DOI: 10.1021/acs.bioconjchem.9b00710] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eugenio Gallo
- Department of Molecular Genetics, University of Toronto, Charles Best Institute, 112 College Street, Toronto, Ontario M5G 1L6, Canada
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34
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Holland JP, Gut M, Klingler S, Fay R, Guillou A. Photochemical Reactions in the Synthesis of Protein-Drug Conjugates. Chemistry 2019; 26:33-48. [PMID: 31599057 DOI: 10.1002/chem.201904059] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 12/15/2022]
Abstract
The ability to modify biologically active molecules such as antibodies with drug molecules, fluorophores or radionuclides is crucial in drug discovery and target identification. Classic chemistry used for protein functionalisation relies almost exclusively on thermochemically mediated reactions. Our recent experiments have begun to explore the use of photochemistry to effect rapid and efficient protein functionalisation. This article introduces some of the principles and objectives of using photochemically activated reagents for protein ligation. The concept of simultaneous photoradiosynthesis of radiolabelled antibodies for use in molecular imaging is introduced as a working example. Notably, the goal of producing functionalised proteins in the absence of pre-association (non-covalent ligand-protein binding) introduces requirements that are distinct from the more regular use of photoactive groups in photoaffinity labelling. With this in mind, the chemistry of thirteen different classes of photoactivatable reagents that react through the formation of intermediate carbenes, electrophiles, dienes, or radicals, is assessed.
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Affiliation(s)
- Jason P Holland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Melanie Gut
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Simon Klingler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Rachael Fay
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amaury Guillou
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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35
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Obaid G, Bano S, Mallidi S, Broekgaarden M, Kuriakose J, Silber Z, Bulin AL, Wang Y, Mai Z, Jin W, Simeone D, Hasan T. Impacting Pancreatic Cancer Therapy in Heterotypic in Vitro Organoids and in Vivo Tumors with Specificity-Tuned, NIR-Activable Photoimmunonanoconjugates: Towards Conquering Desmoplasia? NANO LETTERS 2019; 19:7573-7587. [PMID: 31518145 PMCID: PMC6934365 DOI: 10.1021/acs.nanolett.9b00859] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Despite untiring efforts to develop therapies for pancreatic ductal adenocarcinoma (PDAC), survival statistics remain dismal, necessitating distinct approaches. Photodynamic priming (PDP), which improves drug delivery and combination regimens, as well as tumor photodestruction are key attributes of photodynamic therapy (PDT), making it a distinctive clinical option for PDAC. Localized, high-payload nanomedicine-assisted delivery of photosensitizers (PSs), with molecular specificity and controlled photoactivation, thus becomes critical in order to reduce collateral toxicity during more expansive photodynamic activation procedures with curative intent. As such, targeted photoactivable lipid-based nanomedicines are an ideal candidate but have failed to provide greater than two-fold cancer cell selectivity, if at all, due to their extensive multivariant physical, optical, and chemical complexity. Here, we report (1) a systematic multivariant tuning approach to engineer (Cet, anti-EGFR mAb) photoimmunonanoconjugates (PINs), and (2) stroma-rich heterotypic PDAC in vitro and in vivo models incorporating patient-derived pancreatic cancer-associated fibroblasts (PCAFs) that recapitulate the desmoplasia observed in the clinic. These offer a comprehensive, disease-specific framework for the development of Cet-PINs. Specificity-tuning of the PINs, in terms of PS lipid anchoring, electrostatic modulation, Cet orientation, and Cet surface densities, achieved ∼16-fold binding specificities and rapid penetration of the heterotypic organoids within 1 h, thereby providing a ∼16-fold enhancement in molecular targeted NIR photodestruction. As a demonstration of their inherent amenability for multifunctionality, encapsulation of high payloads of gemcitabine hydrochloride, 5-fluorouracil, and oxaliplatin within the Cet-PINs further improved their antitumor efficacy in the heterotypic organoids. In heterotypic desmoplastic tumors, the Cet-PINs efficiently penetrated up to 470 μm away from blood vessels, and photodynamic activation resulted in substantial tumor necrosis, which was not elicited in T47D tumors (low EGFR) or when using untargeted constructs in both tumor types. Photodynamic activation of the Cet-PINs in the heterotypic desmoplastic tumors resulted in collagen photomodulation, with a 1.5-fold reduction in collagen density, suggesting that PDP may also hold potential for conquering desmoplasia. The in vivo safety profile of photodynamic activation of the Cet-PINs was also substantially improved, as compared to the untargeted constructs. While treatment using the Cet-PINs did not cause any detriment to the mice's health or to healthy proximal tissue, photodynamic activation of untargeted constructs induced severe acute cachexia and weight loss in all treated mice, with substantial peripheral skin necrosis, muscle necrosis, and bowel perforation. This study is the first report demonstrating the true value of molecular targeting for NIR-activable PINs. These constructs integrate high payload delivery, efficient photodestruction, molecular precision, and collagen photomodulation in desmoplastic PDAC tumors in a single treatment using a single construct. Such combined PIN platforms and heterocellular models open up an array of further multiplexed combination therapies to synergistically control desmoplastic tumor progression and extend PDAC patient survival.
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Affiliation(s)
- Girgis Obaid
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shazia Bano
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Srivalleesha Mallidi
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Mans Broekgaarden
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jerrin Kuriakose
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Zachary Silber
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Anne-Laure Bulin
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Yucheng Wang
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Zhiming Mai
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Wendong Jin
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Diane Simeone
- Department of Surgery and Department of Pathology, Perlmutter Cancer Center, New York University Langone Health, New York, New York 10016, United States
| | - Tayyaba Hasan
- Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, United States
- Division of Health Sciences and Technology, Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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36
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Stiller C, Aghelpasand H, Frick T, Westerlund K, Ahmadian A, Karlström AE. Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates. Bioconjug Chem 2019; 30:2790-2798. [PMID: 31609586 DOI: 10.1021/acs.bioconjchem.9b00548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Antibody-DNA conjugates are powerful tools for DNA-assisted protein analysis. Growing usage of these methods demands efficient production of high-quality conjugates. We developed an easy and fast synthesis route yielding covalent antibody-DNA conjugates with a defined conjugation site and low batch-to-batch variability. We utilize the Z domain from protein A, containing the unnatural amino acid 4-benzoylphenylalanine (BPA) for photoaffinity labeling of the antibodies' Fc region. Z(xBPA) domains are C-terminally modified with triple-glycine (G3)-modified DNA-oligonucleotides via enzymatic Sortase A coupling. We show reliable modification of the most commonly used IgG's. To prove our conjugates' functionality, we detected antibody-antigen binding events in an assay called Droplet Barcode Sequencing for Protein analysis (DBS-Pro). It confirms not only retained functionality for both conjugate parts but also the potential of using DBS-Pro for quantifying protein abundances. As intermediates are easily storable and our approach is modular, it offers a convenient strategy for screening various antibody-DNA conjugates using the same starting material.
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Affiliation(s)
- Christiane Stiller
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
| | - Hooman Aghelpasand
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Tobias Frick
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Kristina Westerlund
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
| | - Afshin Ahmadian
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, Science for Life Laboratory , 171 65 Solna , Sweden
| | - Amelie Eriksson Karlström
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health , KTH Royal Institute of Technology, AlbaNova University Center , 106 91 Stockholm , Sweden
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37
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Abstract
Antibodies can be developed to directly inhibit almost any protein, but their inability to enter the cytosol limits inhibitory antibodies to membrane-associated or extracellular targets. Developing a cytosolic antibody delivery system would offer unique opportunities to directly inhibit and study intracellular protein function. Here we demonstrate that IgG antibodies that are conjugated with anionic polypeptides (ApPs) can be complexed with cationic lipids originally designed for nucleic acid delivery through electrostatic interactions, enabling close to 90% cytosolic delivery efficiency with only 500 nM IgG. The ApP is fused to a small photoreactive antibody-binding domain (pAbBD) that can be site-specifically photocrosslinked to nearly all off-the-shelf IgGs, enabling easy exchange of cargo IgGs. We show that cytosolically delivered IgGs can inhibit the drug efflux pump multidrug resistance-associated protein 1 (MRP1) and the transcription factor NFκB. This work establishes an approach for using existing antibody collections to modulate intracellular protein function.
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38
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Cremers GAO, Rosier BJHM, Riera Brillas R, Albertazzi L, de Greef TFA. Efficient Small-Scale Conjugation of DNA to Primary Antibodies for Multiplexed Cellular Targeting. Bioconjug Chem 2019; 30:2384-2392. [PMID: 31438665 PMCID: PMC6753658 DOI: 10.1021/acs.bioconjchem.9b00490] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The
combination of the specificity of antibodies and the programmability
of DNA nanotechnology has provided the scientific community with a
powerful tool to label and unambiguously distinguish a large number
of subcellular targets using fluorescence-based read-out methods.
Whereas primary antibodies are commercially available for a large
class of targets, a general stoichiometric site-selective DNA labeling
strategy for this affinity reagent is lacking. Here we present a universal,
site-selective conjugation method using a small photo-cross-linkable
protein G adaptor that allows labeling of antibodies of different
host species with a controlled number of short oligonucleotides (ODNs).
Importantly, we illustrate that this conjugation method can be directly
performed on commercially available primary antibodies on a small
scale and without cross-reactivity towards bovine serum albumin. In
addition, we present a general benchtop-compatible strategy to purify
DNA-labeled antibodies without a loss of function. The application
of protein G-ODN-labeled primary antibodies is demonstrated by employing
three well-known methods for detecting subcellular targets using fluorescence
read-out, including flow cytometry, DNA-PAINT, and dSTORM. This work
thus establishes a general and efficient platform for the synthesis
of a library of unique ODN–antibody conjugates, facilitating
the broader use of DNA-based programmable tags for multiplexed labeling
to identify subcellular features with nanometer precision and improving
our understanding of cellular structure and function.
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Affiliation(s)
- Glenn A O Cremers
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands.,Computational Biology Group, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Bas J H M Rosier
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands.,Computational Biology Group, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Roger Riera Brillas
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands.,Molecular Biosensing for Medical Diagnostics, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Lorenzo Albertazzi
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands.,Molecular Biosensing for Medical Diagnostics, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands.,Computational Biology Group, Department of Biomedical Engineering , Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven , The Netherlands.,Institute for Molecules and Materials , Radboud University , Heyendaalseweg 135 , 6525 AJ Nijmegen , The Netherlands
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Yamada K, Ito Y. Recent Chemical Approaches for Site‐Specific Conjugation of Native Antibodies: Technologies toward Next‐Generation Antibody–Drug Conjugates. Chembiochem 2019; 20:2729-2737. [DOI: 10.1002/cbic.201900178] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Kei Yamada
- Ajinomoto Co., Inc. 1-1 Suzuki-Cho Kawasaki-Ku Kawasaki-Shi Kanagawa 210-8681 Japan
- Department of Chemistry and BioscienceGraduate School of Science and EngineeringKagoshima University 1-21-35 Korimoto Kagoshima 890-0065 Japan
| | - Yuji Ito
- Department of Chemistry and BioscienceGraduate School of Science and EngineeringKagoshima University 1-21-35 Korimoto Kagoshima 890-0065 Japan
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40
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Site-Specific Photocrosslinking to Immunoglobulin G Using Photoreactive Antibody-Binding Domains. Methods Mol Biol 2019; 2033:275-286. [PMID: 31332760 DOI: 10.1007/978-1-4939-9654-4_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The high specificity and strong binding affinity of antibodies, most commonly immunoglobulin G (IgG), have led to their use in a wide range of research, diagnostic and therapeutic applications. Many of these applications require the antibody to be labeled with additional chemical or biological moieties. Here, we describe a method for the rapid and site-specific labeling of nearly any "off-the-shelf" IgG. Our method utilizes small photoreactive antibody-binding domains (pAbBDs) that are produced by modifying the IgG-binding domains of Protein A and Protein G with the unnatural amino acid benzoylphenylalanine (BPA). The pAbBDs are covalently linked to IgG heavy chains upon exposure to ultraviolet light. Fusion of pAbBDs to a given protein of interest or conjugation of pAbBDs with drugs, fluorophores, and/or other chemical moieties, enables the facile production of a diverse range of antibody conjugates.
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41
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Ackerman DS, Altun B, Kolodieznyi D, Bruchez MP, Tsourkas A, Jarvik JW. Antibody-Linked Fluorogen-Activating Proteins for Antigen Detection and Cell Ablation. Bioconjug Chem 2018; 30:63-69. [PMID: 30543409 DOI: 10.1021/acs.bioconjchem.8b00720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate selective labeling of cell surface proteins using fluorogen-activating proteins (FAPs) conjugated to standard immunoglobulins (IgGs). Conjugation was achieved with a polypeptide reagent comprised of an N-terminal photoactivatable Fc-binding domain and a C-terminal FAP domain. The resulting FAP-antibody conjugates were effective agents for protein detection and cell ablation in cultured mammalian cells and for visualizing cell-cell contacts using a tethered fluorogen assay. Because our approach allows FAP-antibody conjugates to be generated for most currently available IgGs, it should have broad utility for experimental and therapeutic applications.
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Affiliation(s)
| | - Burcin Altun
- Department of Bioengineering , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | | | | | - Andrew Tsourkas
- Department of Bioengineering , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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42
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Vance N, Zacharias N, Ultsch M, Li G, Fourie A, Liu P, LaFrance-Vanasse J, Ernst JA, Sandoval W, Kozak KR, Phillips G, Wang W, Sadowsky J. Development, Optimization, and Structural Characterization of an Efficient Peptide-Based Photoaffinity Cross-Linking Reaction for Generation of Homogeneous Conjugates from Wild-Type Antibodies. Bioconjug Chem 2018; 30:148-160. [DOI: 10.1021/acs.bioconjchem.8b00809] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Nicholas Vance
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Neelie Zacharias
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mark Ultsch
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Guangmin Li
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Aimee Fourie
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter Liu
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Julien LaFrance-Vanasse
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James A. Ernst
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Wendy Sandoval
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Katherine R. Kozak
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Gail Phillips
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Weiru Wang
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jack Sadowsky
- Research & Early Development, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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43
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Yu C, Tang J, Loredo A, Chen Y, Jung SY, Jain A, Gordon A, Xiao H. Proximity-Induced Site-Specific Antibody Conjugation. Bioconjug Chem 2018; 29:3522-3526. [DOI: 10.1021/acs.bioconjchem.8b00680] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | | | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Antrix Jain
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
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44
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Park J, Lee Y, Ko BJ, Yoo TH. Peptide-Directed Photo-Cross-Linking for Site-Specific Conjugation of IgG. Bioconjug Chem 2018; 29:3240-3244. [PMID: 30179444 DOI: 10.1021/acs.bioconjchem.8b00515] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conjugation of antibody has expanded its applications in therapeutics and diagnostics, and various methods have been developed based on chemical or enzymatic reactions. However, the majority of them have focused on synthetic molecules such as small molecules, nucleic acids, or synthetic materials, but site-specific conjugation of antibody with protein cargo has rarely been demonstrated. In this Communication, we report a PEptide-DIrected Photo-cross-linking (PEDIP) reaction for site-specific conjugation of IgG with protein using an Fc-binding peptide and a photoreactive amino acid analogue, and demonstrate this method by developing an immunotoxin composed of a Her2-targeting IgG (trastuzumab) and an engineered Pseudomonas exotoxin A (PE24). The ADP-ribosylation of eukaryotic elongation factor-2 by the bacterial toxin inhibits the ribosomal translation of protein, and the trastuzumab-PE24 conjugate exhibited the cytotoxicity toward Her2-overexpressing cell lines. The PEDIP reaction can also be applied for many other types of cargo with slight modifications of the method.
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Affiliation(s)
| | | | - Byoung Joon Ko
- New Drug Development Center , Osong Medical Innovative Foundation , 123 Osongsaengmyeong-ro , Osong-eup, Cheongju , 28160 , Korea
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45
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Rosier BJHM, Cremers GAO, Engelen W, Merkx M, Brunsveld L, de Greef TFA. Incorporation of native antibodies and Fc-fusion proteins on DNA nanostructures via a modular conjugation strategy. Chem Commun (Camb) 2018; 53:7393-7396. [PMID: 28617516 PMCID: PMC5708335 DOI: 10.1039/c7cc04178k] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A photocrosslinkable protein G adapter was used to site-specifically conjugate complex native proteins to oligonucleotides, allowing for efficient incorporation on DNA origami nanostructures.
A photocrosslinkable protein G variant was used as an adapter protein to covalently and site-specifically conjugate an antibody and an Fc-fusion protein to an oligonucleotide. This modular approach enables straightforward decoration of DNA nanostructures with complex native proteins while retaining their innate binding affinity, allowing precise control over the nanoscale spatial organization of such proteins for in vitro and in vivo biomedical applications.
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Affiliation(s)
- Bas J H M Rosier
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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46
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Antos JM, Ingram J, Fang T, Pishesha N, Truttmann MC, Ploegh HL. Site-Specific Protein Labeling via Sortase-Mediated Transpeptidation. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2017; 89:15.3.1-15.3.19. [PMID: 28762490 PMCID: PMC5810355 DOI: 10.1002/cpps.38] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Strategies for site-specific protein modification are highly desirable for the construction of conjugates containing non-genetically-encoded functional groups. Ideally, these strategies should proceed under mild conditions, and be compatible with a wide range of protein targets and non-natural moieties. The transpeptidation reaction catalyzed by bacterial sortases is a prominent strategy for protein derivatization that possesses these features. Naturally occurring or engineered variants of sortase A from Staphylococcus aureus catalyze a ligation reaction between a five-amino-acid substrate motif (LPXTG) and oligoglycine nucleophiles. By pairing proteins and synthetic peptides that possess these ligation handles, it is possible to install modifications onto the protein N- or C-terminus in site-specific fashion. As described in this unit, the successful implementation of sortase-mediated labeling involves straightforward solid-phase synthesis and molecular biology techniques, and this method is compatible with proteins in solution or on the surface of live cells. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- John M Antos
- Department of Chemistry, Western Washington University, Bellingham, Washington
| | - Jessica Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Tao Fang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Matthias C Truttmann
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
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47
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Orientation and characterization of immobilized antibodies for improved immunoassays (Review). Biointerphases 2017; 12:02D301. [DOI: 10.1116/1.4978435] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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48
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King J, Bouvet M, Singh G, Williams J. Improving theranostics in pancreatic cancer. J Surg Oncol 2017; 116:104-113. [PMID: 28513912 DOI: 10.1002/jso.24625] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/05/2017] [Indexed: 01/03/2023]
Abstract
BACKGROUND Pancreatic cancer is the fourth most deadly cancer in the United States, and is expected to be the second most deadly by 2030. The major difficulty in treating pancreatic cancer is the late onset of symptoms. Generally, patients show metastatic disease by the time of diagnosis, with a survival rate of 5% beyond 5 years. In patients without metastatic disease, surgical resection increases 5 year survival rate to 25%. The remaining 75% succumb to undetected metastases. Clearly, improvements to both detection, surgical intervention, and therapeutic strategies will be needed to improve patient outcome in pancreatic cancer. METHODS Recent literature has been surveyed and atomic models of new therapeutic approaches were generated. RESULTS AND CONCLUSIONS Here, we focus on the recent progress employing monoclonal antibodies (mAbs) to target pancreatic cancer associated markers, and more specifically on recent chemical and protein engineering efforts to improve the homogeneity, stability, and administration of mAbs to precisely deliver imaging agents and cytotoxins to sites of disease.
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Affiliation(s)
- Jeremy King
- Department of Molecular Medicine, Beckman Research Institute at City of Hope, Duarte, California
| | - Michael Bouvet
- Department of Surgery, University of California San Diego, San Diego, California
| | | | - John Williams
- Department of Molecular Medicine, Beckman Research Institute at City of Hope, Duarte, California
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49
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Fc-specific biotinylation of antibody using an engineered photoactivatable Z–Biotin and its biosensing application. Anal Chim Acta 2017; 949:76-82. [DOI: 10.1016/j.aca.2016.10.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 10/19/2016] [Accepted: 10/26/2016] [Indexed: 01/01/2023]
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50
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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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