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Chiawpanit C, Wathikthinnakorn M, Sawasdee N, Phanthaphol N, Sujjitjoon J, Junking M, Yamabhai M, Panaampon J, Yenchitsomanus PT, Panya A. Precision immunotherapy for cholangiocarcinoma: Pioneering the use of human-derived anti-cMET single chain variable fragment in anti-cMET chimeric antigen receptor (CAR) NK cells. Int Immunopharmacol 2024; 136:112273. [PMID: 38810311 DOI: 10.1016/j.intimp.2024.112273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Cholangiocarcinoma (CCA) presents a significant clinical challenge which is often identified in advanced stages, therby restricting the effectiveness of surgical interventions for most patients. The high incidence of cancer recurrence and resistance to chemotherapy further contribute to a bleak prognosis and low survival rates. To address this pressing need for effective therapeutic strategies, our study focuses on the development of an innovative cellular immunotherapy, specifically utilizing chimeric antigen receptor (CAR)-engineered natural killer (NK) cells designed to target the cMET receptor tyrosine kinase. In this investigation, we initiated the screening of a phage library displaying human single-chain variable fragment (ScFv) to identify novel ScFv molecules with specificity for cMET. Remarkably, ScFv11, ScFv72, and ScFv114 demonstrated exceptional binding affinity, confirmed by molecular docking analysis. These selected ScFvs, in addition to the well-established anti-cMET ScFvA, were integrated into a CAR cassette harboring CD28 transmembrane region-41BB-CD3ζ domains. The resulting anti-cMET CAR constructs were transduced into NK-92 cells, generating potent anti-cMET CAR-NK-92 cells. To assess the specificity and efficacy of these engineered cells, we employed KKU213A cells with high cMET expression and KKU055 cells with low cMET levels. Notably, co-culture of anti-cMET CAR-NK-92 cells with KKU213A cells resulted in significantly increased cell death, whereas no such effect was observed with KKU055 cells. In summary, our study identified cMET as a promising therapeutic target for CCA. The NK-92 cells, armed with the anti-cMET CAR molecule, have shown strong ability to kill cancer cells specifically, indicating their potential as a promising treatment for CCA in the future.
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Affiliation(s)
- Chutipa Chiawpanit
- Cell Engineering for Cancer Therapy Research Group, Chiang Mai University, Chiang Mai, Thailand; Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand; Office of Research Administration, Chiang Mai University, Chiang Mai, Thailand
| | - Methi Wathikthinnakorn
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nunghathai Sawasdee
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nattaporn Phanthaphol
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jatuporn Sujjitjoon
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Mutita Junking
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agriculture Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Jutatip Panaampon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Aussara Panya
- Cell Engineering for Cancer Therapy Research Group, Chiang Mai University, Chiang Mai, Thailand; Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
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Tadokoro T, Tsuboi H, Nakamura K, Hayakawa T, Ohmura R, Kato I, Inoue M, Tsunoda S, Niizuma S, Okada Y, Otsuguro S, Maenaka K. Thermostability and binding properties of single-chained Fv fragments derived from therapeutic antibodies. Protein Sci 2024; 33:e5084. [PMID: 38923711 PMCID: PMC11201803 DOI: 10.1002/pro.5084] [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: 02/10/2024] [Revised: 05/15/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Small antibody fragments have recently been used as alternatives to full-length monoclonal antibodies in therapeutic applications. One of the most popular fragment antibodies is single-chain fragment variables (scFvs), consisting of variable heavy (VH) and variable light (VL) domains linked by a flexible peptide linker. scFvs have small molecular sizes, which enables good tissue penetration and low immunogenicity. Despite these advantages, the use of scFvs, especially for therapeutic purpose, is still limited because of the difficulty to regulate the binding activity and conformational stability. In this study, we constructed and analyzed 10 scFv fragments derived from 10 representatives of FDA-approved mAbs to evaluate their physicochemical properties. Differential scanning calorimetry analysis showed that scFvs exhibited relatively high but varied thermostability, from 50 to 70°C of melting temperatures, and different unfolding cooperativity. Surface plasmon resonance analysis revealed that scFvs fragments that exhibit high stability and cooperative unfolding likely tend to maintain antigen binding. This study demonstrated the comprehensive physicochemical properties of scFvs derived from FDA-approved antibodies, providing insights into antibody design and development.
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Affiliation(s)
- Takashi Tadokoro
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Harumi Tsuboi
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Kota Nakamura
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Tetsushi Hayakawa
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Reo Ohmura
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Izumi Kato
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Masaki Inoue
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical SciencesKobe Gakuin UniversityKobeJapan
| | - Shin‐ichi Tsunoda
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical SciencesKobe Gakuin UniversityKobeJapan
| | - Sayaka Niizuma
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Yukari Okada
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Satoko Otsuguro
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan
- Institute for Vaccine Research and Development (HU‐IVReD)Hokkaido UniversitySapporoJapan
- Global Station for Biosurfaces and Drug DiscoveryHokkaido UniversitySapporoJapan
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3
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Castillo-Corujo A, Uchida Y, Saaranen MJ, Ruddock LW. Escherichia coli Cytoplasmic Expression of Disulfide-Bonded Proteins: Side-by-Side Comparison between Two Competing Strategies. J Microbiol Biotechnol 2024; 34:1126-1134. [PMID: 38563095 PMCID: PMC11180911 DOI: 10.4014/jmb.2311.11025] [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: 11/17/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
The production of disulfide bond-containing recombinant proteins in Escherichia coli has traditionally been done by either refolding from inclusion bodies or by targeting the protein to the periplasm. However, both approaches have limitations. Two broad strategies were developed to allow the production of proteins with disulfide bonds in the cytoplasm of E. coli: i) engineered strains with deletions in the disulfide reduction pathways, e.g. SHuffle, and ii) the co-expression of oxidative folding catalysts, e.g. CyDisCo. However, to our knowledge, the relative effectiveness of these strategies has not been properly evaluated. Here, we systematically compare the purified yields of 14 different proteins of interest (POI) that contain disulfide bonds in their native state when expressed in both systems. We also compared the effects of different background strains, commonly used promoters, and two media types: defined and rich autoinduction. In rich autoinduction media, POI which can be produced in a soluble (non-native) state without a system for disulfide bond formation were produced in higher purified yields from SHuffle, whereas all other proteins were produced in higher purified yields using CyDisCo. In chemically defined media, purified yields were at least 10x higher in all cases using CyDisCo. In addition, the quality of the three POI tested was superior when produced using CyDisCo.
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Affiliation(s)
- Angel Castillo-Corujo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| | - Yuko Uchida
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| | - Mirva J. Saaranen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
| | - Lloyd W. Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland
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4
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Castillo-Corujo A, Saaranen MJ, Ruddock LW. Cytoplasmic production of Fabs in chemically defined media in fed-batch fermentation. Protein Expr Purif 2024; 215:106404. [PMID: 37979630 DOI: 10.1016/j.pep.2023.106404] [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: 09/18/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/20/2023]
Abstract
Fragment of antigen-binding region (Fab) of antibodies are important biomolecules, with a broad spectrum of functionality in the biomedical field. While full length antibodies are usually produced in mammalian cells, the smaller size, lack of N-glycosylation and less complex structure of Fabs make production in microbial cell factories feasible. Since Fabs contain disulfide bonds, such production is often done in the periplasm, but there the formation of the inter-molecular disulfide bond between light and heavy chains can be problematic. Here we studied the use of the CyDisCo system (cytoplasmic disulfide bond formation in E. coli) to express two Fabs (Herceptin and Maa48) in the cytoplasm of E. coli in fed-batch fermentation using a generic chemically defined media. We were able to solubly express both Fabs with purified yields of 565 mg/L (Maa48) and 660 mg/L (Herceptin) from low density fermentation. Both proteins exhibited CD spectra consistent with natively folded protein and both were biologically active. To our knowledge this is the first demonstration of high-level production of biological active Fabs in the cytoplasm of E. coli in industrially relevant fermentation conditions.
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Affiliation(s)
| | - Mirva J Saaranen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Lloyd W Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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5
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Knödler M, Frank K, Kerpen L, Buyel JF. Design, optimization, production and activity testing of recombinant immunotoxins expressed in plants and plant cells for the treatment of monocytic leukemia. Bioengineered 2023; 14:2244235. [PMID: 37598369 PMCID: PMC10444015 DOI: 10.1080/21655979.2023.2244235] [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: 11/29/2022] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 08/22/2023] Open
Abstract
Antibody-drug conjugates (ADCs) can improve therapeutic indices compared to plain monoclonal antibodies (mAbs). However, ADC synthesis is complex because the components are produced separately in CHO cells (mAb) and often by chemical synthesis (drug). They are individually purified, coupled, and then the ADC is purified, increasing production costs compared to regular mAbs. In contrast, it is easier to produce recombinant fusion proteins consisting of an antibody derivative, linker and proteinaceous toxin, i.e. a recombinant immunotoxin (RIT). Plants are capable of the post-translational modifications needed for functional antibodies and can also express active protein toxins such as the recombinant mistletoe lectin viscumin, which is not possible in prokaryotes and mammalian cells respectively. Here, we used Nicotiana benthamiana and N. tabacum plants as well as tobacco BY-2 cell-based plant cell packs (PCPs) to produce effective RITs targeting CD64 as required for the treatment of myelomonocytic leukemia. We compared RITs with different subcellular targeting signals, linkers, and proteinaceous toxins. The accumulation of selected candidates was improved to ~ 40 mg kg-1 wet biomass using a design of experiments approach, and corresponding proteins were isolated with a purity of ~ 80% using an optimized affinity chromatography method with an overall yield of ~ 84%. One anti-CD64 targeted viscumin-based drug candidate was characterized in terms of storage stability and cytotoxicity test in vitro using human myelomonocytic leukemia cell lines. We identified bottlenecks in the plant-based expression platform that require further improvement and assessed critical process parameters that should be considered during process development for plant-made RITs.
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Affiliation(s)
- Matthias Knödler
- Bioprocess Engineering, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Katharina Frank
- Bioprocess Engineering, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Lucy Kerpen
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Johannes Felix Buyel
- Bioprocess Engineering, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Aachen, Germany
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
- University of Natural Resources and Life Sciences, Vienna (BOKU), Department of Biotechnology (DBT), Institute of Bioprocess Science and Engineering (IBSE), Vienna, Austria
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6
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Komatsu S, Ohno H, Saito H. Target-dependent RNA polymerase as universal platform for gene expression control in response to intracellular molecules. Nat Commun 2023; 14:7256. [PMID: 37978180 PMCID: PMC10656481 DOI: 10.1038/s41467-023-42802-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023] Open
Abstract
Controlling gene expression in response to specific molecules is an essential technique for regulating cellular functions. However, current platforms with transcription and translation regulators have a limited number of detectable molecules to induce gene expression. Here to address these issues, we present a Target-dependent RNA polymerase (TdRNAP) that can induce RNA transcription in response to the intracellular target specifically recognized by single antibody. By substituting the fused antibody, we demonstrate that TdRNAPs respond to a wide variety of molecules, including peptides, proteins, RNA, and small molecules, and produce desired transcripts in human cells. Furthermore, we show that multiple TdRNAPs can construct orthogonal and multilayer genetic circuits. Finally, we apply TdRNAP to achieve cell-specific genome editing that is autonomously triggered by detecting the target gene product. TdRNAP can expand the molecular variety for controlling gene expression and provide the genetic toolbox for bioengineering and future therapeutic applications.
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Affiliation(s)
- Shodai Komatsu
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hirohisa Ohno
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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7
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Byun KT, Kim B, Cho J, Lee I, Lee MG, Park D, Kang TB, Won HS, Kim CG. Development of an Anti-HER2 Single-Chain Variable Antibody Fragment Construct for High-Yield Soluble Expression in Escherichia coli and One-Step Chromatographic Purification. Biomolecules 2023; 13:1508. [PMID: 37892190 PMCID: PMC10605039 DOI: 10.3390/biom13101508] [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: 09/19/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Although single-chain variable fragment (scFv) is recognized as a highly versatile scaffold of recombinant antibody fragment molecules, its overexpression in Escherichia coli often leads to the formation of inclusion bodies. To address this issue, we devised and tested four different constructs, named v21, v22, v23 and v24, for producing anti-human epidermal growth factor receptor 2 (HER2) scFv. Among them, the v24 construct obtained from N-terminal fusion of maltose-binding protein (MBP) and subsequent tobacco etch virus protease (TEV) was identified as the most efficient construct for the production of anti-HER2 scFv. Aided by an MBP tag, high-yield soluble expression was ensured and soluble scFv was liberated in cells via autonomous proteolytic cleavage by endogenously expressed TEV. The isolated scFv containing a C-terminal hexahistidine tag was purified through a one-step purification via nickel-affinity chromatography. The purified scFv exhibited a strong (nanomolar Kd) affinity to HER2 both in vitro and in cells. Structural and functional stabilities of the scFv during storage for more than one month were also assured. Given the great utility of anti-HER2 scFv as a basic platform for developing therapeutic and diagnostic agents for cancers, the v24 construct and methods presented in this study are expected to provide a better manufacturing system for producing anti-HER2 scFv with various industrial applications.
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Affiliation(s)
- Kyu Tae Byun
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (K.T.B.); (B.K.)
| | - Boram Kim
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (K.T.B.); (B.K.)
| | - Junmin Cho
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (K.T.B.); (B.K.)
| | - Inbeom Lee
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (K.T.B.); (B.K.)
| | - Myung Gu Lee
- Konkukbio Inc., Konkuk University, Chungju 27478, Republic of Korea
| | - Dongsun Park
- Department of Biology Education, Korea National University of Education, Cheongju 28173, Republic of Korea
| | - Tae-Bong Kang
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (K.T.B.); (B.K.)
- BK21 Project Team, Department of Applied Life Science, Graduate School, Konkuk University, Chungju 27478, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (K.T.B.); (B.K.)
- BK21 Project Team, Department of Applied Life Science, Graduate School, Konkuk University, Chungju 27478, Republic of Korea
| | - Chan Gil Kim
- Department of Biotechnology, Research Institute (RIBHS), College of Biomedical and Health Science, Konkuk University, Chungju 27478, Republic of Korea; (K.T.B.); (B.K.)
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8
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Tungekar AA, Ruddock LW. Design of an alternate antibody fragment format that can be produced in the cytoplasm of Escherichia coli. Sci Rep 2023; 13:14188. [PMID: 37648872 PMCID: PMC10469194 DOI: 10.1038/s41598-023-41525-3] [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: 05/23/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023] Open
Abstract
With increased accessibility and tissue penetration, smaller antibody formats such as antibody fragments (Fab) and single chain variable fragments (scFv) show potential as effective and low-cost choices to full-length antibodies. These formats derived from the modular architecture of antibodies could prove to be game changers for certain therapeutic and diagnostic applications. Microbial hosts have shown tremendous promise as production hosts for antibody fragment formats. However, low target protein yields coupled with the complexity of protein folding result in production limitations. Here, we report an alternative antibody fragment format 'FabH3' designed to overcome some key bottlenecks associated with the folding and production of Fabs. The FabH3 molecule is based on the Fab format with the constant domains replaced by engineered immunoglobulin G1 (IgG1) CH3 domains capable of heterodimerization based on the electrostatic steering approach. We show that this alternative antibody fragment format can be efficiently produced in the cytoplasm of E. coli using the catalyzed disulfide-bond formation system (CyDisCo) in a natively folded state with higher soluble yields than its Fab counterpart and a comparable binding affinity against the target antigen.
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Affiliation(s)
- Aatir A Tungekar
- Protein and Structural Biology Research Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Lloyd W Ruddock
- Protein and Structural Biology Research Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland.
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Sarén T, Saronio G, Marti Torrell P, Zhu X, Thelander J, Andersson Y, Hofström C, Nestor M, Dimberg A, Persson H, Ramachandran M, Yu D, Essand M. Complementarity-determining region clustering may cause CAR-T cell dysfunction. Nat Commun 2023; 14:4732. [PMID: 37563127 PMCID: PMC10415375 DOI: 10.1038/s41467-023-40303-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/19/2023] [Indexed: 08/12/2023] Open
Abstract
Chimeric antigen receptor (CAR)-T cell therapy is rapidly advancing as cancer treatment, however, designing an optimal CAR remains challenging. A single-chain variable fragment (scFv) is generally used as CAR targeting moiety, wherein the complementarity-determining regions (CDRs) define its specificity. We report here that the CDR loops can cause CAR clustering, leading to antigen-independent tonic signalling and subsequent CAR-T cell dysfunction. We show via CARs incorporating scFvs with identical framework and varying CDR sequences that CARs may cluster on the T cell surface, which leads to antigen-independent CAR-T cell activation, characterized by increased cell size and interferon (IFN)-γ secretion. This results in CAR-T cell exhaustion, activation-induced cell death and reduced responsiveness to target-antigen-expressing tumour cells. CDR mutagenesis confirms that the CAR-clustering is mediated by CDR-loops. In summary, antigen-independent tonic signalling can be induced by CDR-mediated CAR clustering, which could not be predicted from the scFv sequences, but could be tested for by evaluating the activity of unstimulated CAR-T cells.
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Affiliation(s)
- Tina Sarén
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Giulia Saronio
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Paula Marti Torrell
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Xu Zhu
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Josefin Thelander
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Yasmin Andersson
- Royal Institute of Technology (KTH), Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Camilla Hofström
- Royal Institute of Technology (KTH), Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Marika Nestor
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Anna Dimberg
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Helena Persson
- Royal Institute of Technology (KTH), Drug Discovery and Development Platform, Science for Life Laboratory, Solna, Sweden
| | - Mohanraj Ramachandran
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Di Yu
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden.
| | - Magnus Essand
- Uppsala University, Dept Immunology, Genetics, Pathology, Science for Life Laboratory, Uppsala, Sweden.
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10
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Recombinant antibodies by phage display for bioanalytical applications. Biosens Bioelectron 2023; 222:114909. [PMID: 36462427 DOI: 10.1016/j.bios.2022.114909] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 10/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Antibody phage display, aimed at preparing antibodies to defined antigens, is a useful replacement for hybridoma technology. The phage system replaces all work stages that follow animal immunization with simple procedures for manipulating DNA and bacteria. It enables the time needed to generate stable antibody-producing clones to be shortened considerably, making the process noticeably cheaper. Antibodies prepared by phage display undergo several affinity selection steps and can be used as selective receptors in biosensors. This article briefly describes the techniques used in the making of phage antibodies to various antigens. The possibilities and prospects are discussed of using phage antibodies as selective agents in analytical systems, including biosensors.
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11
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Teppert K, Wang X, Anders K, Evaristo C, Lock D, Künkele A. Joining Forces for Cancer Treatment: From "TCR versus CAR" to "TCR and CAR". Int J Mol Sci 2022; 23:ijms232314563. [PMID: 36498890 PMCID: PMC9739809 DOI: 10.3390/ijms232314563] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
T cell-based immunotherapy has demonstrated great therapeutic potential in recent decades, on the one hand, by using tumor-infiltrating lymphocytes (TILs) and, on the other hand, by engineering T cells to obtain anti-tumor specificities through the introduction of either engineered T cell receptors (TCRs) or chimeric antigen receptors (CARs). Given the distinct design of both receptors and the type of antigen that is encountered, the requirements for proper antigen engagement and downstream signal transduction by TCRs and CARs differ. Synapse formation and signal transduction of CAR T cells, despite further refinement of CAR T cell designs, still do not fully recapitulate that of TCR T cells and might limit CAR T cell persistence and functionality. Thus, deep knowledge about the molecular differences in CAR and TCR T cell signaling would greatly advance the further optimization of CAR designs and elucidate under which circumstances a combination of both receptors would improve the functionality of T cells for cancer treatment. Herein, we provide a comprehensive review about similarities and differences by directly comparing the architecture, synapse formation and signaling of TCRs and CARs, highlighting the knowns and unknowns. In the second part of the review, we discuss the current status of combining CAR and TCR technologies, encouraging a change in perspective from "TCR versus CAR" to "TCR and CAR".
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Affiliation(s)
- Karin Teppert
- Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Xueting Wang
- Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Kathleen Anders
- German Cancer Consortium (DKTK), 10117 Berlin, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - César Evaristo
- Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Dominik Lock
- Miltenyi Biotec B.V. & Co. KG, 51429 Bergisch Gladbach, Germany
| | - Annette Künkele
- German Cancer Consortium (DKTK), 10117 Berlin, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany
- Correspondence:
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12
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Introduction of a More Glutaredoxin-like Active Site to PDI Results in Competition between Protein Substrate and Glutathione Binding. Antioxidants (Basel) 2022; 11:antiox11101920. [PMID: 36290643 PMCID: PMC9598436 DOI: 10.3390/antiox11101920] [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] [Received: 09/12/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins in the thioredoxin superfamily share a similar fold, contain a -CXXC- active site, and catalyze oxidoreductase reactions by dithiol-disulfide exchange mechanisms. Protein disulfide isomerase (PDI) has two -CGHC- active sites. For in vitro studies, oxidation/reduction of PDI during the catalytic cycle is accomplished with glutathione. Glutathione may act as electron donor/acceptor for PDI also in vivo, but at least for oxidation reactions, GSSG probably is not the major electron acceptor and PDI may not have evolved to react with glutathione with high affinity, but merely having adequate affinity for both glutathione and folding proteins/peptides. Glutaredoxins, on the other hand, have a high affinity for glutathione. They commonly have -CXFC- or -CXYC- active site, where the tyrosine residue forms part of the GSH binding groove. Mutating the active site of PDI to a more glutaredoxin-like motif increased its reactivity with glutathione. All such variants showed an increased rate in GSH-dependent reduction or GSSG-dependent oxidation of the active site, as well as a decreased rate of the native disulfide bond formation, with the magnitude of the effect increasing with glutathione concentration. This suggests that these variants lead to competition in binding between glutathione and folding protein substrates.
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13
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Li L, Wu S, Si Y, Li H, Yin X, Peng D. Single-chain fragment variable produced by phage display technology: Construction, selection, mutation, expression, and recent applications in food safety. Compr Rev Food Sci Food Saf 2022; 21:4354-4377. [PMID: 35904244 DOI: 10.1111/1541-4337.13018] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 01/28/2023]
Abstract
Immunoassays are reliable, efficient, and accurate methods for the analysis of small-molecule harmful substances (such as pesticides, veterinary drugs, and biological toxins) that may be present in food. However, traditional polyclonal and monoclonal antibodies are limited by animal hosts and hinder further development of immunoassays. With the gradual application of phage display technology as an efficient in vitro selection technology, the single-chain fragment variable (scFv) now provides an exciting alternative to traditional antibodies. Efficiently constructed scFv source libraries and specifically designed biopanning schemes can now yield scFvs possessing specific recognition capabilities. A rational mutation strategy further enhances the affinity of scFv, and allows it to reach a level that cannot be achieved by immunization. Finally, appropriate prokaryotic expression measures ensure stable and efficient production of scFv. Therefore, when developing excellent scFvs, it is necessary to focus on three key aspects of this process that include screening, mutation, and expression. In this review, we analyze in detail the preparation and affinity improvement process for scFv and provide insights into the research progress and development trend of scFv-based immunoassay methods for monitoring small-molecule harmful substances.
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Affiliation(s)
- Long Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shuangmin Wu
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yu Si
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Huaming Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaoyang Yin
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Dapeng Peng
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, Hubei, China.,Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, Guangdong, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
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14
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Wang Y, Yuan W, Guo S, Li Q, Chen X, Li C, Liu Q, Sun L, Chen Z, Yuan Z, Luo C, Chen S, Tong S, Nassal M, Wen YM, Wang YX. A 33-residue peptide tag increases solubility and stability of Escherichia coli produced single-chain antibody fragments. Nat Commun 2022; 13:4614. [PMID: 35941164 PMCID: PMC9359998 DOI: 10.1038/s41467-022-32423-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
Single-chain variable fragments (scFvs), composed of variable domains of heavy and light chains of an antibody joined by a linker, share antigen binding capacity with their parental antibody. Due to intrinsically low solubility and stability, only two Escherichia coli-produced scFvs have been approved for therapy. Here we report that a 33-residue peptide, termed P17 tag, increases the solubility of multiple scFvs produced in Escherichia coli SHuffle strain by up to 11.6 fold. Hydrophilic sequence, especially charged residues, but not the predicted α-helical secondary structure of P17 tag, contribute to the solubility enhancement. Notably, the P17 tag elevates the thermostability of scFv as efficiently as intra-domain disulfide bonds. Moreover, a P17-tagged scFv targeting hepatitis B virus surface proteins shows over two-fold higher antigen-binding affinity and virus-neutralizing activity than the untagged version. These data strongly suggest a type I intramolecular chaperone-like activity of the P17 tag. Hence, the P17 tag could benefit the research, production, and application of scFv. Low solubility and stability of Escherichia coli produced single chain variable fragments (scFvs) restrict their applications. Here the authors report a 33-residue peptide tag which simultaneously increases the solubility and thermostability of multiple scFvs produced in Escherichia coli SHuffle strain.
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Affiliation(s)
- Yang Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenjie Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Siqi Guo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, Nanchang University, Nanchang, China
| | - Qiqi Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaomei Chen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qianying Liu
- Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Lei Sun
- Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Zhenguo Chen
- Institutes of Biomedical Science, Fudan University, Shanghai, China
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China
| | - Shijie Chen
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Shuping Tong
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Michael Nassal
- Department of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Freiburg, Germany
| | - Yu-Mei Wen
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yong-Xiang Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
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15
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Extracellular production of an anti-HER2 single-chain variable antibody fragment in Escherichia coli. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Shin C, Kim SS, Jo YH. Extending traditional antibody therapies: Novel discoveries in immunotherapy and clinical applications. Mol Ther Oncolytics 2021; 22:166-179. [PMID: 34514097 PMCID: PMC8416972 DOI: 10.1016/j.omto.2021.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Immunotherapy has been well regarded as one of the safer and antigen-specific anti-cancer treatments compared to first-generation chemotherapy. Since Coley's discovery, researchers focused on engineering novel antibody-based therapies. Including artificial and modified antibodies, such as antibody fragments, antibody-drug conjugates, and synthetic mimetics, the variety of immunotherapy has been rapidly expanding in the last few decades. Genetic and chemical modifications to monoclonal antibody have been brought into academia, in vivo trials, and clinical applications. Here, we have looked around antibodies overall. First, we elucidate the antibody structure and its cytotoxicity mechanisms. Second, types of therapeutic antibodies are presented. Additionally, there is a summarized list of US Food and Drug Administration (FDA)-approved therapeutic antibodies and recent clinical trials. This review provides a comprehensive overview of both the general function of therapeutic antibodies and a few main variations in development, including recent advent with the proposed mechanism of actions, and we introduce types of therapeutic antibodies, clinical trials, and approved commercial immunotherapeutic drugs.
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Affiliation(s)
- Charles Shin
- Chadwick International, Incheon 22002, Republic of Korea
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung Soo Kim
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yong Hwa Jo
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
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17
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Molecular mechanism of amyloidogenic mutations in hypervariable regions of antibody light chains. J Biol Chem 2021; 296:100334. [PMID: 33508322 PMCID: PMC7949129 DOI: 10.1016/j.jbc.2021.100334] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
Systemic light chain (AL) amyloidosis is a fatal protein misfolding disease in which excessive secretion, misfolding, and subsequent aggregation of free antibody light chains eventually lead to deposition of amyloid plaques in various organs. Patient-specific mutations in the antibody VL domain are closely linked to the disease, but the molecular mechanisms by which certain mutations induce misfolding and amyloid aggregation of antibody domains are still poorly understood. Here, we compare a patient VL domain with its nonamyloidogenic germline counterpart and show that, out of the five mutations present, two of them strongly destabilize the protein and induce amyloid fibril formation. Surprisingly, the decisive, disease-causing mutations are located in the highly variable complementarity determining regions (CDRs) but exhibit a strong impact on the dynamics of conserved core regions of the patient VL domain. This effect seems to be based on a deviation from the canonical CDR structures of CDR2 and CDR3 induced by the substitutions. The amyloid-driving mutations are not necessarily involved in propagating fibril formation by providing specific side chain interactions within the fibril structure. Rather, they destabilize the VL domain in a specific way, increasing the dynamics of framework regions, which can then change their conformation to form the fibril core. These findings reveal unexpected influences of CDR-framework interactions on antibody architecture, stability, and amyloid propensity.
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18
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Koçer İ, Cox EC, DeLisa MP, Çelik E. Effects of variable domain orientation on anti-HER2 single-chain variable fragment antibody expressed in the Escherichia coli cytoplasm. Biotechnol Prog 2020; 37:e3102. [PMID: 33190426 DOI: 10.1002/btpr.3102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/04/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Single-chain variable fragment (scFv) antibodies have great potential for a range of applications including as diagnostic and therapeutic agents. However, production of scFvs is challenging because proper folding and activity depend on the formation of two intrachain disulfide bonds that do not readily form in the cytoplasm of living cells. Functional expression in bacteria therefore involves targeting to the more oxidizing periplasm, but yields in this compartment can be limiting due to secretion bottlenecks and the relatively small volume compared to the cytoplasm. In the present study, we evaluated an anti-HER2 scFv, which is specific for human epidermal growth receptor 2 (HER2) overexpressed in breast cancer, for functional expression in the cytoplasm of Escherichia coli strains BL21(DE3) and SHuffle T7 Express, the latter of which is genetically engineered for cytoplasmic disulfide bond formation. Specifically, we observed much greater solubility and binding activity with SHuffle T7 Express cells, which likely resulted from the more oxidative cytoplasm in this strain background. We also found that SHuffle T7 Express cells were capable of supporting high-level soluble production of anti-HER2 scFvs with intact disulfide bonds independent of variable domain orientation, providing further evidence that SHuffle T7 Express is a promising host for laboratory and preparative expression of functional scFv antibodies.
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Affiliation(s)
- İlkay Koçer
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey.,Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Emily C Cox
- Biological and Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA.,Biological and Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey.,Institute of Science, Division of Bioengineering, Hacettepe University, Ankara, Turkey
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19
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Kang TH, Seong BL. Solubility, Stability, and Avidity of Recombinant Antibody Fragments Expressed in Microorganisms. Front Microbiol 2020; 11:1927. [PMID: 33101218 PMCID: PMC7546209 DOI: 10.3389/fmicb.2020.01927] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Solubility of recombinant proteins (i.e., the extent of soluble versus insoluble expression in heterogeneous hosts) is the first checkpoint criterion for determining recombinant protein quality. However, even soluble proteins often fail to represent functional activity because of the involvement of non-functional, misfolded, soluble aggregates, which compromise recombinant protein quality. Therefore, screening of solubility and folding competence is crucial for improving the quality of recombinant proteins, especially for therapeutic applications. The issue is often highlighted especially in bacterial recombinant hosts, since bacterial cytoplasm does not provide an optimal environment for the folding of target proteins of mammalian origin. Antibody fragments, such as single-chain variable fragment (scFv), single-chain antibody (scAb), and fragment antigen binding (Fab), have been utilized for numerous applications such as diagnostics, research reagents, or therapeutics. Antibody fragments can be efficiently expressed in microorganisms so that they offer several advantages for diagnostic applications such as low cost and high yield. However, scFv and scAb fragments have generally lower stability to thermal stress than full-length antibodies, necessitating a judicious combination of designer antibodies, and bacterial hosts harnessed with robust chaperone function. In this review, we discuss efforts on not only the production of antibodies or antibody fragments in microorganisms but also scFv stabilization via (i) directed evolution of variants with increased stability using display systems, (ii) stabilization of the interface between variable regions of heavy (VH) and light (VL) chains through the introduction of a non-native covalent bond between the two chains, (iii) rational engineering of VH-VL pair, based on the structure, and (iv) computational approaches. We also review recent advances in stability design, increase in avidity by multimerization, and maintaining the functional competence of chimeric proteins prompted by various types of chaperones.
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Affiliation(s)
- Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, South Korea
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20
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Ma H, Ó'Fágáin C, O'Kennedy R. Antibody stability: A key to performance - Analysis, influences and improvement. Biochimie 2020; 177:213-225. [PMID: 32891698 DOI: 10.1016/j.biochi.2020.08.019] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 02/01/2023]
Abstract
An antibody's stability greatly influences its performance (i.e. its specificity and affinity). Thus, stability is a major issue for researchers and manufacturers, especially with the increasing use of antibodies in therapeutics, diagnostics and rapid analytical platforms. Here we review antibody stability under five headings: (i) measurement techniques; (ii) stability issues in expression and production (expression, proteolysis, aggregation); (iii) effects of antibody format and engineering on stability and (iv) formulation, drying and storage conditions. We consider more than 100 sources, including patents, and conclude with (v) recommendations to promote antibody stability.
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Affiliation(s)
- Hui Ma
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland
| | - Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland.
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Dublin 9, D09 V2O9, Ireland; Qatar Foundation, Research Complex, And Hamad Bin Khalifa University, Education City, Doha, Qatar
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21
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A robust fractionation method for protein subcellular localization studies in Escherichia coli. Biotechniques 2020; 66:171-178. [PMID: 30987443 DOI: 10.2144/btn-2018-0135] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fractionation in Gram-negative bacteria is used to identify the subcellular localization of proteins, in particular the localization of exported recombinant proteins. The process of cell fractionation can be fraught with cross-contamination issues and often lacks supporting data for fraction purity. Here, we compare three periplasm extraction and two cell disruption techniques in different combinations to investigate which process gives uncontaminated compartments from Escherichia coli. From these data, a robust method named PureFrac was compiled that gives pure periplasmic fractions and a superior recovery of soluble cytoplasmic proteins. The process extracts periplasm using cold osmotic shock with magnesium, prior to sonication and ultracentrifugation to separate the cytoplasm from insoluble material. This method handles cells cultivated in various conditions and allows preparation of active proteins in their respective compartments.
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22
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An ultra-stable cytoplasmic antibody engineered for in vivo applications. Nat Commun 2020; 11:336. [PMID: 31953402 PMCID: PMC6969036 DOI: 10.1038/s41467-019-13654-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/08/2019] [Indexed: 11/16/2022] Open
Abstract
Targeting cytoplasmic protein–protein interactions with antibodies remains technically challenging, since antibodies expressed in the cytosol frequently form insoluble aggregates. Existing engineering methods are based on the notion that the estimated net charge at pH 7.4 affects stability; as such, they are unable to overcome this problem. Herein, we report a versatile method for engineering an ultra-stable cytoplasmic antibody (STAND), with a strong estimated net negative charge at pH 6.6, by fusing peptide tags with a highly negative charge and a low isoelectric point. Without the need for complicated amino acid substitutions, we convert aggregation-prone antibodies to STANDs that are useful for inhibiting in vivo transmitter release, modulating animal behaviour, and inhibiting in vivo cancer proliferation driven by mutated Kras—long recognised as an “undruggable” oncogenic protein. The STAND method shows promise for targeting endogenous cytoplasmic proteins in basic biology and for developing future disease treatments. Antibodies expressed in the cytosol often form insoluble aggregates, which makes it hard to target intracellular proteins. Here the authors engineer an ultra-stable cytoplasmic antibody (STAND) with a low isoelectric point that can be used in vivo.
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23
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Applications of catalyzed cytoplasmic disulfide bond formation. Biochem Soc Trans 2019; 47:1223-1231. [DOI: 10.1042/bst20190088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/09/2019] [Accepted: 09/20/2019] [Indexed: 12/14/2022]
Abstract
Abstract
Disulfide bond formation is an essential post-translational modification required for many proteins to attain their native, functional structure. The formation of disulfide bonds, otherwise known as oxidative protein folding, occurs in the endoplasmic reticulum and mitochondrial inter-membrane space in eukaryotes and the periplasm of prokaryotes. While there are differences in the molecular mechanisms of oxidative folding in different compartments, it can essentially be broken down into two steps, disulfide formation and disulfide isomerization. For both steps, catalysts exist in all compartments where native disulfide bond formation occurs. Due to the importance of disulfide bonds for a plethora of proteins, considerable effort has been made to generate cell factories which can make them more efficiently and cheaper. Recently synthetic biology has been used to transfer catalysts of native disulfide bond formation into the cytoplasm of prokaryotes such as Escherichia coli. While these engineered systems cannot yet rival natural systems in the range and complexity of disulfide-bonded proteins that can be made, a growing range of proteins have been made successfully and yields of homogenously folded eukaryotic proteins exceeding g/l yields have been obtained. This review will briefly give an overview of such systems, the uses reported to date and areas of future potential development, including combining with engineered systems for cytoplasmic glycosylation.
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24
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Horga LG, Halliwell S, Castiñeiras TS, Wyre C, Matos CFRO, Yovcheva DS, Kent R, Morra R, Williams SG, Smith DC, Dixon N. Tuning recombinant protein expression to match secretion capacity. Microb Cell Fact 2018; 17:199. [PMID: 30577801 PMCID: PMC6303999 DOI: 10.1186/s12934-018-1047-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/14/2018] [Indexed: 03/08/2023] Open
Abstract
Background The secretion of recombinant disulfide-bond containing proteins into the periplasm of Gram-negative bacterial hosts, such as E. coli, has many advantages that can facilitate product isolation, quality and activity. However, the secretion machinery of E. coli has a limited capacity and can become overloaded, leading to cytoplasmic retention of product; which can negatively impact cell viability and biomass accumulation. Fine control over recombinant gene expression offers the potential to avoid this overload by matching expression levels to the host secretion capacity. Results Here we report the application of the RiboTite gene expression control system to achieve this by finely controlling cellular expression levels. The level of control afforded by this system allows cell viability to be maintained, permitting production of high-quality, active product with enhanced volumetric titres. Conclusions The methods and systems reported expand the tools available for the production of disulfide-bond containing proteins, including antibody fragments, in bacterial hosts. Electronic supplementary material The online version of this article (10.1186/s12934-018-1047-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luminita Gabriela Horga
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Samantha Halliwell
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | | | | | | | | | - Ross Kent
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | - Rosa Morra
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK
| | | | | | - Neil Dixon
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, M1 7DN, UK.
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25
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Biterova E, Esmaeeli M, Alanen HI, Saaranen M, Ruddock LW. Structures of Angptl3 and Angptl4, modulators of triglyceride levels and coronary artery disease. Sci Rep 2018; 8:6752. [PMID: 29713054 PMCID: PMC5928061 DOI: 10.1038/s41598-018-25237-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/12/2018] [Indexed: 01/01/2023] Open
Abstract
Coronary artery disease is the most common cause of death globally and is linked to a number of risk factors including serum low density lipoprotein, high density lipoprotein, triglycerides and lipoprotein(a). Recently two proteins, angiopoietin-like protein 3 and 4, have emerged from genetic studies as being factors that significantly modulate plasma triglyceride levels and coronary artery disease. The exact function and mechanism of action of both proteins remains to be elucidated, however, mutations in these proteins results in up to 34% reduction in coronary artery disease and inhibition of function results in reduced plasma triglyceride levels. Here we report the crystal structures of the fibrinogen-like domains of both proteins. These structures offer new insights into the reported loss of function mutations, the mechanisms of action of the proteins and open up the possibility for the rational design of low molecular weight inhibitors for intervention in coronary artery disease.
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Affiliation(s)
- Ekaterina Biterova
- Faculty of Biochemistry and Molecular Biology and Biocenter Oulu, University of Oulu, Oulu, 90220, Finland
| | - Mariam Esmaeeli
- Faculty of Biochemistry and Molecular Biology and Biocenter Oulu, University of Oulu, Oulu, 90220, Finland
- Department of Molecular Enzymology, University of Potsdam, 14476, Potsdam, Germany
| | - Heli I Alanen
- Faculty of Biochemistry and Molecular Biology and Biocenter Oulu, University of Oulu, Oulu, 90220, Finland
| | - Mirva Saaranen
- Faculty of Biochemistry and Molecular Biology and Biocenter Oulu, University of Oulu, Oulu, 90220, Finland
| | - Lloyd W Ruddock
- Faculty of Biochemistry and Molecular Biology and Biocenter Oulu, University of Oulu, Oulu, 90220, Finland.
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