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Tučs A, Ito T, Kurumida Y, Kawada S, Nakazawa H, Saito Y, Umetsu M, Tsuda K. Extensive antibody search with whole spectrum black-box optimization. Sci Rep 2024; 14:552. [PMID: 38177656 PMCID: PMC10767033 DOI: 10.1038/s41598-023-51095-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/30/2023] [Indexed: 01/06/2024] Open
Abstract
In designing functional biological sequences with machine learning, the activity predictor tends to be inaccurate due to shortage of data. Top ranked sequences are thus unlikely to contain effective ones. This paper proposes to take prediction stability into account to provide domain experts with a reasonable list of sequences to choose from. In our approach, multiple prediction models are trained by subsampling the training set and the multi-objective optimization problem, where one objective is the average activity and the other is the standard deviation, is solved. The Pareto front represents a list of sequences with the whole spectrum of activity and stability. Using this method, we designed VHH (Variable domain of Heavy chain of Heavy chain) antibodies based on the dataset obtained from deep mutational screening. To solve multi-objective optimization, we employed our sequence design software MOQA that uses quantum annealing. By applying several selection criteria to 19,778 designed sequences, five sequences were selected for wet-lab validation. One sequence, 16 mutations away from the closest training sequence, was successfully expressed and found to possess desired binding specificity. Our whole spectrum approach provides a balanced way of dealing with the prediction uncertainty, and can possibly be applied to extensive search of functional sequences.
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Affiliation(s)
- Andrejs Tučs
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yoichi Kurumida
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Department of Data Science, School of Frontier Engineering, Kitasato University, Sagamihara, Japan
| | - Sakiya Kawada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yutaka Saito
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- RIKEN Center for Advanced Intelligence Project, RIKEN, Tokyo, 103-0027, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan
- Department of Data Science, School of Frontier Engineering, Kitasato University, Sagamihara, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan.
- RIKEN Center for Advanced Intelligence Project, RIKEN, Tokyo, 103-0027, Japan.
| | - Koji Tsuda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- RIKEN Center for Advanced Intelligence Project, RIKEN, Tokyo, 103-0027, Japan.
- Center for Basic Research on Materials, National Institute for Materials Science (NIMS), Tsukuba, Japan.
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Nakazawa H, Katsuki T, Matsui T, Tsugita A, Yokoyama T, Ito T, Kawada S, Tanaka Y, Umetsu M. Synthesis of epitope-targeting nanobody based on native protein-protein interactions for FtsZ filamentation suppressor. Biotechnol J 2023; 18:e2300039. [PMID: 37458140 DOI: 10.1002/biot.202300039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Phage display and biopanning are powerful tools for generating binding molecules for a specific target. However, the selection process based only on binding affinity provides no assurance for the antibody's affinity to the target epitope. In this study, we propose a molecular-evolution approach guided by native protein-protein interactions to generate epitope-targeting antibodies. The binding-site sequence in a native protein was grafted into a complementarity-determining region (CDR) in the nanobody, and a nonrelated CDR loop (in the grafted nanobody) was randomized to create a phage display library. In this construction of nanobodies by integrating graft and evolution technology (CAnIGET method), suitable grafting of the functional sequence added functionality to the nanobody, and the molecular-evolution approach enhanced the binding function to inhibit the native protein-protein interactions. To apply for biological tool with growth screening, model nanobodies with an affinity for filamenting temperature-sensitive mutant Z (FtsZ) from Staphylococcus aureus were constructed and completely inhibited the polymerization of FtsZ as a function. Consequently, the expression of these nanobodies drastically decreased the cell division rate. We demonstrate the potential of the CAnIGET method with the use of native protein-protein interactions for steady epitope-specific evolutionary engineering.
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Affiliation(s)
- Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Taiji Katsuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Takashi Matsui
- Department of Physics, School of Science, Kitasato University, Sagamihara, Japan
| | - Atsushi Tsugita
- Department of Applied Biological Molecular Science, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Takeshi Yokoyama
- Department of Applied Biological Molecular Science, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Sakiya Kawada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yoshikazu Tanaka
- Department of Applied Biological Molecular Science, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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Tamaru Y, Nakanishi S, Tanaka K, Umetsu M, Nakazawa H, Sugiyama A, Ito T, Shimokawa N, Takagi M. Recent research advances on non-linear phenomena in various biosystems. J Biosci Bioeng 2023:S1389-1723(23)00107-X. [PMID: 37246137 DOI: 10.1016/j.jbiosc.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/03/2023] [Accepted: 03/22/2023] [Indexed: 05/30/2023]
Abstract
All biological phenomena can be classified as open, dissipative and non-linear. Moreover, the most typical phenomena are associated with non-linearity, dissipation and openness in biological systems. In this review article, four research topics on non-linear biosystems are described to show the examples from various biological systems. First, membrane dynamics of a lipid bilayer for the cell membrane is described. Since the cell membrane separates the inside of the cell from the outside, self-organizing systems that form spatial patterns on membranes often depend on non-linear dynamics. Second, various data banks based on recent genomics analysis supply the data including vast functional proteins from many organisms and their variable species. Since the proteins existing in nature are only a very small part of the space represented by amino acid sequence, success of mutagenesis-based molecular evolution approach crucially depends on preparing a library with high enrichment of functional proteins. Third, photosynthetic organisms depend on ambient light, the regular and irregular changes of which have a significant impact on photosynthetic processes. The light-driven process proceeds through many redox couples in the cyanobacteria constituting chain of redox reactions. Forth topics focuses on a vertebrate model, the zebrafish, which can help to understand, predict and control the chaos of complex biological systems. In particular, during early developmental stages, developmental differentiation occurs dynamically from a fertilized egg to divided and mature cells. These exciting fields of complexity, chaos, and non-linear science have experienced impressive growth in recent decades. Finally, future directions for non-liner biosystems are presented.
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Affiliation(s)
- Yutaka Tamaru
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan.
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kenya Tanaka
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Aruto Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Adschiri T, Takami S, Umetsu M, Ohara S, Naka T, Minami K, Hojo D, Togashi T, Arita T, Taguchi M, Itoh M, Aoki N, Seong G, Tomai T, Yoko A. Supercritical Hydrothermal Reactions for Material Synthesis. BCSJ 2023. [DOI: 10.1246/bcsj.20220295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Tadafumi Adschiri
- WPI – Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
- New Industry Creation Hatchery Center, Tohoku University, 6-6-10 Aoba, Aramaki, Aoba-ku, Sendai 980-8579
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
| | - Seiichi Takami
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603
| | - Mitsuo Umetsu
- Graduate School of Engineering, Tohoku University, 6-6-11 Aramaki Aza Aoba, Aoba-ku, Sendai 980-8579
| | - Satoshi Ohara
- Joining and Welding Research Institute, Osaka University, 11-1 Mihogaoka, Osaka, 567-0047
| | - Takashi Naka
- National Institute of Materials Sciences (NIMS), 1-2-1 Sengen, Tsukuba 305-0047
| | - Kimitaka Minami
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8565
| | - Daisuke Hojo
- WPI – Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
| | - Takanari Togashi
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata, 990-8560
| | - Toshihiko Arita
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
| | - Minori Taguchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
| | - Masahiro Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
| | - Nobuaki Aoki
- WPI – Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
| | - Gimyeong Seong
- New Industry Creation Hatchery Center, Tohoku University, 6-6-10 Aoba, Aramaki, Aoba-ku, Sendai 980-8579
| | - Takaaki Tomai
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
| | - Akira Yoko
- WPI – Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577
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Ito T, Nguyen TD, Saito Y, Kurumida Y, Nakazawa H, Kawada S, Nishi H, Tsuda K, Kameda T, Umetsu M. Selection of target-binding proteins from the information of weakly enriched phage display libraries by deep sequencing and machine learning. MAbs 2023; 15:2168470. [PMID: 36683172 PMCID: PMC9872955 DOI: 10.1080/19420862.2023.2168470] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Despite the advances in surface-display systems for directed evolution, variants with high affinity are not always enriched due to undesirable biases that increase target-unrelated variants during biopanning. Here, our goal was to design a library containing improved variants from the information of the "weakly enriched" library where functional variants were weakly enriched. Deep sequencing for the previous biopanning result, where no functional antibody mimetics were experimentally identified, revealed that weak enrichment was partly due to undesirable biases during phage infection and amplification steps. The clustering analysis of the deep sequencing data from appropriate steps revealed no distinct sequence patterns, but a Bayesian machine learning model trained with the selected deep sequencing data supplied nine clusters with distinct sequence patterns. Phage libraries were designed on the basis of the sequence patterns identified, and four improved variants with target-specific affinity (EC50 = 80-277 nM) were identified by biopanning. The selection and use of deep sequencing data without undesirable bias enabled us to extract the information on prospective variants. In summary, the use of appropriate deep sequencing data and machine learning with the sequence data has the possibility of finding sequence space where functional variants are enriched.
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Affiliation(s)
- Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Thuy Duong Nguyen
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Yutaka Saito
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan,AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan,Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
| | - Yoichi Kurumida
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Sakiya Kawada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Hafumi Nishi
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Sendai, Japan,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Faculty of Core Research, Ochanomizu University, Tokyo, Japan
| | - Koji Tsuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan,Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan,Research and Services Division of Materials Data and Integrated Systems, National Institute for Materials Science, Tsukuba, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan,Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan,CONTACT Tomoshi Kameda Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan,Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan,Mitsuo Umetsu Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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6
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Masakari Y, Hara C, Nakazawa H, Ichiyanagi A, Umetsu M. Comparison of the stability of Mucor-derived flavin adenine dinucleotide-dependent glucose dehydrogenase and glucose oxidase. J Biosci Bioeng 2022; 134:307-310. [PMID: 35927131 DOI: 10.1016/j.jbiosc.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 10/16/2022]
Abstract
Long-term stability at near-body temperature is important for continuous glucose monitoring (CGM) sensors. However, the stability of enzymes used in CGM sensors has often been evaluated by measuring their melting temperature (Tm) values and by short heat treatment but not at around 37 °C. Glucose oxidase (GOD) is used in current CGM sensors. In this study, we evaluated the stability of modified Mucor-derived flavin adenine dinucleotide-dependent glucose dehydrogenase (designated Mr144-297) with improved thermal stability at medium to high temperatures and compared it with that of GOD. The Tm value of Mr144-297 was 61.6 ± 0.3 °C and was similar to that of GOD (61.4 ± 1.2 °C). However, Mr144-297 was clearly more stable than GOD at 40 °C and 55 °C. At 37 °C, the stability of a carbon electrode with immobilized Mr144-297 was higher than that of an electrode with GOD. Our data indicate that Mr144-297 is a more suitable enzyme for CGM sensors than is GOD.
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Affiliation(s)
- Yosuke Masakari
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda City, Chiba 278-0037, Japan; Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
| | - Chiaki Hara
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda City, Chiba 278-0037, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Atsushi Ichiyanagi
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda City, Chiba 278-0037, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
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7
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Ito Y, Ishigami M, Terai G, Nakamura Y, Hashiba N, Nishi T, Nakazawa H, Hasunuma T, Asai K, Umetsu M, Ishii J, Kondo A. A streamlined strain engineering workflow with genome-wide screening detects enhanced protein secretion in Komagataella phaffii. Commun Biol 2022; 5:561. [PMID: 35676418 PMCID: PMC9177720 DOI: 10.1038/s42003-022-03475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/11/2022] [Indexed: 11/26/2022] Open
Abstract
Expression of secreted recombinant proteins burdens the protein secretion machinery, limiting production. Here, we describe an approach to improving protein production by the non-conventional yeast Komagataella phaffii comprised of genome-wide screening for effective gene disruptions, combining them in a single strain, and recovering growth reduction by adaptive evolution. For the screen, we designed a multiwell-formatted, streamlined workflow to high-throughput assay of secretion of a single-chain small antibody, which is cumbersome to detect but serves as a good model of proteins that are difficult to secrete. Using the consolidated screening system, we evaluated >19,000 mutant strains from a mutant library prepared by a modified random gene-disruption method, and identified six factors for which disruption led to increased antibody production. We then combined the disruptions, up to quadruple gene knockouts, which appeared to contribute independently, in a single strain and observed an additive effect. Target protein and promoter were basically interchangeable for the effects of knockout genes screened. We finally used adaptive evolution to recover reduced cell growth by multiple gene knockouts and examine the possibility for further enhancing protein secretion. Our successful, three-part approach holds promise as a method for improving protein production by non-conventional microorganisms.
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Affiliation(s)
- Yoichiro Ito
- Engineering Biology Research Center, Kobe University, Kobe, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Misa Ishigami
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan
| | - Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Yasuyuki Nakamura
- Engineering Biology Research Center, Kobe University, Kobe, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Noriko Hashiba
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe, Japan
| | - Teruyuki Nishi
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
- Bio-Pharma Research Laboratories, Kaneka Corporation, Takasago, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, Kobe, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, Kobe, Japan.
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, Kobe, Japan.
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.
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Saito Y, Oikawa M, Sato T, Nakazawa H, Ito T, Kameda T, Tsuda K, Umetsu M. Machine-Learning-Guided Library Design Cycle for Directed Evolution of Enzymes: The Effects of Training Data Composition on Sequence Space Exploration. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yutaka Saito
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Misaki Oikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Takumi Sato
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Koji Tsuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
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9
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Ando Y, Nakazawa H, Miura D, Otake M, Umetsu M. Enzymatic ligation of an antibody and arginine 9 peptide for efficient and cell-specific siRNA delivery. Sci Rep 2021; 11:21882. [PMID: 34750461 PMCID: PMC8575896 DOI: 10.1038/s41598-021-01331-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
A fusion protein comprising an antibody and a cationic peptide, such as arginine-9 (R9), is a candidate molecule for efficient and cell-specific delivery of siRNA into cells in order to reduce the side effects of nucleic acid drugs. However, their expression in bacterial hosts, required for their development, often fails, impeding research progress. In this study, we separately prepared anti-EGFR nanobodies with the K-tag sequence MRHKGS at the C-terminus and R9 with the Q-tag sequence LLQG at the N-terminus, and enzymatically ligated them in vitro by microbial transglutaminase to generate Nanobody-R9, which is not expressed as a fused protein in E. coli. Nanobody-R9 was synthesized at a maximum binding efficiency of 85.1%, without changing the binding affinity of the nanobody for the antigen. Nanobody-R9 successfully delivered siRNA into the cells, and the cellular influx of siRNA increased with increase in the ratio of Nanobody-R9 to siRNA. We further demonstrated that the Nanobody-R9-siRNA complex, at a 30:1 ratio, induced an approximately 58.6% reduction in the amount of target protein due to RNAi in mRNA compared to lipofectamine.
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Affiliation(s)
- Yu Ando
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan.
| | - Daisuke Miura
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Maho Otake
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-1, Aramaki, Aoba-ku, Sendai, 980-8579, Japan.
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10
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Ito T, Nishi H, Kameda T, Yoshida M, Fukazawa R, Kawada S, Nakazawa H, Umetsu M. Combination Informatic and Experimental Approach for Selecting Scaffold Proteins for Development as Antibody Mimetics. CHEM LETT 2021. [DOI: 10.1246/cl.210443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Hafumi Nishi
- Department of Applied Information Sciences, Graduate School of Information Science, Tohoku University, 6-3-09 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Faculty of Core Research, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Mayu Yoshida
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Reito Fukazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Sakiya Kawada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
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11
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Onodera M, Sueyoshi K, Umetsu M. Fluorescence Quenching by Complex of a DNA Aptamer and Porphyrin for Sensitive Detection of Porphyrins by Capillary Electrophoresis. CHEM LETT 2021. [DOI: 10.1246/cl.200729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mari Onodera
- Tohoku University, 6-6-11 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
- Panasonic Corporation, 8-21-1 Ginza, Chuo-ku, Tokyo 140-0061, Japan
| | - Kenji Sueyoshi
- Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Mitsuo Umetsu
- Tohoku University, 6-6-11 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
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12
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Irumagawa S, Kobayashi K, Saito Y, Miyata T, Umetsu M, Kameda T, Arai R. Rational thermostabilisation of four-helix bundle dimeric de novo proteins. Sci Rep 2021; 11:7526. [PMID: 33824364 PMCID: PMC8024369 DOI: 10.1038/s41598-021-86952-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/22/2021] [Indexed: 11/29/2022] Open
Abstract
The stability of proteins is an important factor for industrial and medical applications. Improving protein stability is one of the main subjects in protein engineering. In a previous study, we improved the stability of a four-helix bundle dimeric de novo protein (WA20) by five mutations. The stabilised mutant (H26L/G28S/N34L/V71L/E78L, SUWA) showed an extremely high denaturation midpoint temperature (Tm). Although SUWA is a remarkably hyperstable protein, in protein design and engineering, it is an attractive challenge to rationally explore more stable mutants. In this study, we predicted stabilising mutations of WA20 by in silico saturation mutagenesis and molecular dynamics simulation, and experimentally confirmed three stabilising mutations of WA20 (N22A, N22E, and H86K). The stability of a double mutant (N22A/H86K, rationally optimised WA20, ROWA) was greatly improved compared with WA20 (ΔTm = 10.6 °C). The model structures suggested that N22A enhances the stability of the α-helices and N22E and H86K contribute to salt-bridge formation for protein stabilisation. These mutations were also added to SUWA and improved its Tm. Remarkably, the most stable mutant of SUWA (N22E/H86K, rationally optimised SUWA, ROSA) showed the highest Tm (129.0 °C). These new thermostable mutants will be useful as a component of protein nanobuilding blocks to construct supramolecular protein complexes.
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Affiliation(s)
- Shin Irumagawa
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano, 390-8621, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan
| | - Kaito Kobayashi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
| | - Yutaka Saito
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, 169-8555, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Takeshi Miyata
- Department of Biochemistry and Biotechnology, Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan
| | - Ryoichi Arai
- Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan.
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano, 390-8621, Japan.
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, 386-8567, Japan.
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13
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Ito T, Nishi H, Duong Nguyen T, Saito Y, Kameda T, Nakazawa H, Tsuda K, Umetsu M. Application of Next-Generation Sequencing Analysis in the Directed Evolution for Creating Antibody Mimic. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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14
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Kobayashi S, Shioya K, Seki Y, Matsumura T, Kanari Y, Shimatani Y, Nakazawa H, Umetsu M, Kataoka S, Nakamura T. Abstract 689: Anti-tumor activity of Bifidobacterium secreting dual specific T cell redirecting antibody against EGFR/HER3-expressing cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Anti-cancer therapies targeting EGFR family, including monoclonal antibodies and kinase inhibitors, are the state of art for solid tumors such as colorectal and non-small cell lung cancers. T cell redirecting bispecific antibodies are a promising approach for cancer immune therapy, whereas their application is limited to hematological malignancy due to adverse events caused by the systemic exposure to highly immunologically active molecule.
To avoid the immunological adverse events, we have created a recombinant Bifidobacterium (APS002) that specifically colonizes in solid tumor and continuously secretes T cell redirecting antibody. The antibody was designed to form a diabody based on the sequence of dual specific antibody for EGFR/HER3 and CD3.
The diabody (termed DBERB1) comprises the equal amount of two polypeptides, anti-h CD3 (VL) - anti-EGFR/hHER3 (VH) and anti-hEGFR/hHER3 (VL) - anti-hCD3 (VH), respectively. DBERB1 bound to human EGFR and HER3, and human CD3. DBERB1 demonstrated potent cytotoxic activities against EGFR- and HER3-expressing human colon cancer HCT116 cells in the presence of human peripheral blood mononuclear cells (hPBMC) with EC50 values of 3 - 9 × 10−12 M. When APS002 was i.v. dosed to HCT116 tumor-bearing SCID mice inoculated with hPBMC, APS002 colonized only in the tumor and DBERB1 was detected in the tumors but not in the plasma. The growth of HCT116 tumors was significantly suppressed by APS002 but not by Bifidobacterium transfected with control vector.
In conclusion, our study in the mouse model indicates that APS002 is a novel and an extremely potent anti-cancer agent distributed only in the tumor. We are currently preparing for pre-clinical studies for the future clinical trials.
Citation Format: Satoshi Kobayashi, Koichiro Shioya, Yuji Seki, Tomio Matsumura, Yasuyoshi Kanari, Yuko Shimatani, Hikaru Nakazawa, Mitsuo Umetsu, Shiro Kataoka, Takaaki Nakamura. Anti-tumor activity of Bifidobacterium secreting dual specific T cell redirecting antibody against EGFR/HER3-expressing cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 689.
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Affiliation(s)
| | | | - Yuji Seki
- 1Anaeropharma Science, Inc., Matsumoto, Japan
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15
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Nakazawa H, Onodera-Sugano T, Sugiyama A, Tanaka Y, Hattori T, Niide T, Ogata H, Asano R, Kumagai I, Umetsu M. Association behavior and control of the quality of cancer therapeutic bispecific diabodies expressed in Escherichia coli. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Asano R, Hosokawa K, Taki S, Konno S, Shimomura I, Ogata H, Okada M, Arai K, Onitsuka M, Omasa T, Nakanishi T, Umetsu M, Kumagai I. Build-up functionalization of anti-EGFR × anti-CD3 bispecific diabodies by integrating high-affinity mutants and functional molecular formats. Sci Rep 2020; 10:4913. [PMID: 32188928 PMCID: PMC7080790 DOI: 10.1038/s41598-020-61840-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/04/2020] [Indexed: 12/26/2022] Open
Abstract
Designing non-natural antibody formats is a practical method for developing highly functional next-generation antibody drugs, particularly for improving the therapeutic efficacy of cancer treatments. One approach is constructing bispecific antibodies (bsAbs). We previously reported a functional humanized bispecific diabody (bsDb) that targeted epidermal growth factor receptor and CD3 (hEx3-Db). We enhanced its cytotoxicity by constructing an Fc fusion protein and rearranging order of the V domain. In this study, we created an additional functional bsAb, by integrating the molecular formats of bsAb and high-affinity mutants previously isolated by phage display in the form of Fv. Introducing the high-affinity mutations into bsDbs successfully increased their affinities and enhanced their cytotoxicity in vitro and in vivo. However, there were some limitations to affinity maturation of bsDb by integrating high-affinity Fv mutants, particularly in Fc-fused bsDb with intrinsic high affinity, because of their bivalency. The tetramers fractionated from the bsDb mutant exhibited the highest in vitro growth inhibition among the small bsAbs and was comparable to the in vivo anti-tumor effects of Fc-fused bsDbs. This molecule shows cost-efficient bacterial production and high therapeutic potential.
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Affiliation(s)
- Ryutaro Asano
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan. .,Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan.
| | - Katsuhiro Hosokawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Shintaro Taki
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Shota Konno
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Ippei Shimomura
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Hiromi Ogata
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Mai Okada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Kyoko Arai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Masayoshi Onitsuka
- Institute of Technology and Science, Tokushima University, Tokushima, 770-8506, Japan
| | - Takeshi Omasa
- Institute of Technology and Science, Tokushima University, Tokushima, 770-8506, Japan
| | - Takeshi Nakanishi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan.
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Saito Y, Oikawa M, Nakazawa H, Sato T, Kameda T, Tsuda K, Umetsu M. Can Machine Learning Guide Directed Evolution of Functional Proteins. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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18
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Kameda T, Kobayashi K, Irumagawa S, Arai R, Saito Y, Miyata T, Umetsu M. Evaluation the Protein Stability by Molecular Dynamics Simulation. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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19
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Ueda A, Umetsu M, Nakanishi T, Hashikami K, Nakazawa H, Hattori S, Asano R, Kumagai I. Chemically Crosslinked Bispecific Antibodies for Cancer Therapy: Breaking from the Structural Restrictions of the Genetic Fusion Approach. Int J Mol Sci 2020; 21:ijms21030711. [PMID: 31973200 PMCID: PMC7037651 DOI: 10.3390/ijms21030711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/02/2022] Open
Abstract
Antibodies are composed of structurally and functionally independent domains that can be used as building blocks to construct different types of chimeric protein-format molecules. However, the generally used genetic fusion and chemical approaches restrict the types of structures that can be formed and do not give an ideal degree of homogeneity. In this study, we combined mutation techniques with chemical conjugation to construct a variety of homogeneous bivalent and bispecific antibodies. First, building modules without lysine residues—which can be chemical conjugation sites—were generated by means of genetic mutation. Specific mutated residues in the lysine-free modules were then re-mutated to lysine residues. Chemical conjugation at the recovered lysine sites enabled the construction of homogeneous bivalent and bispecific antibodies from block modules that could not have been so arranged by genetic fusion approaches. Molecular evolution and bioinformatics techniques assisted in finding viable alternatives to the lysine residues that did not deactivate the block modules. Multiple candidates for re-mutation positions offer a wide variety of possible steric arrangements of block modules, and appropriate linkages between block modules can generate highly bioactive bispecific antibodies. Here, we propose the effectiveness of the lysine-free block module design for site-specific chemical conjugation to form a variety of types of homogeneous chimeric protein-format molecule with a finely tuned structure and function.
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Affiliation(s)
| | - Mitsuo Umetsu
- Correspondence: (M.U.); (I.K.); Tel.: +81-22-795-7274 (M.U.); +81-22-795-7275 (I.K.)
| | | | | | | | | | | | - Izumi Kumagai
- Correspondence: (M.U.); (I.K.); Tel.: +81-22-795-7274 (M.U.); +81-22-795-7275 (I.K.)
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20
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Hemmi S, Asano R, Kimura K, Umetsu M, Nakanishi T, Kumagai I, Makabe K. Construction of a circularly connected VHH bispecific antibody (cyclobody) for the desirable positioning of antigen-binding sites. Biochem Biophys Res Commun 2019; 523:72-77. [PMID: 31831177 DOI: 10.1016/j.bbrc.2019.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 12/04/2019] [Indexed: 12/30/2022]
Abstract
A bispecific antibody (bsAb) is an emerging class of next-generation biological therapeutics. BsAbs are engineered antibodies possessing dual antigen-binding paratopes in one molecule. The circular backbone topology has never been demonstrated, although an enormous number of bispecific constructs have been proposed. The circular topology is potentially beneficial for fixing the orientation of two paratopes and protection from exopeptidase digestion. We construct herein a circularly connected bispecific VHH, termed cyclobody, using the split-intein circular ligation of peptides and proteins. The constructed cyclobodies are protected from proteolysis with a retained bispecificity. The anti-EGFR × anti-GFP cyclobody can specifically stain EGFR-positive cells with GFP. The anti-EGFR × anti-CD16 cyclobody shows cytotoxic activity against EGFR-positive cancer cells with comparative activity of a tandem VHH construct. Successful demonstration of a new topology for the bispecific antibody will expand the construction strategy for developing antibody-based drugs and reagents.
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Affiliation(s)
- Saki Hemmi
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 183-8538, Japan
| | - Kouki Kimura
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 183-8538, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11-606 Aoba-yama, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Takeshi Nakanishi
- Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Izumi Kumagai
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 183-8538, Japan
| | - Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata, 992-8510, Japan.
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21
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Nakazawa H, Umetsu M, Hirose T, Hattori T, Kumagai I. Identification of Indium Tin Oxide Nanoparticle-Binding Peptides via Phage Display and Biopanning Under Various Buffer Conditions. Protein Pept Lett 2019; 27:557-566. [PMID: 31729292 DOI: 10.2174/0929866526666191113151934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/04/2019] [Accepted: 10/08/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND By recent advances in phage-display approaches, many oligopeptides exhibiting binding affinities for metal oxides have been identified. Indium tin oxide is one of the most widely used conductive oxides, because it has a large band gap of 3.7-4.0 eV. In recent years, there have been reports about several ITO-based biosensors. Development of an ITO binding interface for the clustering of sensor proteins without complex bioconjugates is required. OBJECTIVE In this article, we aimed to identify peptides that bind to indium tin oxide nanoparticles via different binding mechanisms. METHODS Indium tin oxide nanoparticles binding peptide ware selected using phage display and biopanning against indium tin oxide, under five different buffer conditions and these peptides characterized about binding affinity and specificity. RESULTS Three types of indium tin oxide nanoparticles-binding peptides were selected from 10 types of peptide candidates identified in phage display and biopanning. These included ITOBP8, which had an acidic isoelectric point, and was identified when a buffer containing guanidine was used, and ITOBP6 and ITOBP7, which contained a His-His-Lys sequence at their N-termini, and were identified when a highly concentrated phosphate elution buffer with a low ionic strength was used. Among these peptides, ITOBP6 exhibited the strongest indium tin oxide nanoparticlesbinding affinity (dissociation constant, 585 nmol/L; amount of protein bound at saturation, 17.5 nmol/m 2 - particles). CONCLUSION These results indicate that peptides with specific binding properties can be obtained through careful selection of the buffer conditions in which the biopanning procedure is performed.
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Affiliation(s)
- Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Tatsuya Hirose
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Takamitsu Hattori
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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22
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Sasaki Y, Sato Y, Takahashi T, Umetsu M, Iki N. Capillary electrophoretic reactor for estimation of spontaneous dissociation rate of Trypsin-Aprotinin complex. Anal Biochem 2019; 585:113406. [PMID: 31445899 DOI: 10.1016/j.ab.2019.113406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 11/25/2022]
Abstract
A capillary electrophoretic reactor was used to analyze the dissociation kinetics of an enzyme-inhibitor complex in a homogeneous solution without immobilization. The complex consisting of trypsin (Try) and aprotinin (Apr) was used as the model. Capillary electrophoresis provided a reaction field for Try-Apr complex to dissociate through the steady removal of free Try and Apr from the Try-Apr zone. By analyzing the dependence of peak height of Try-Apr on separation time, the dissociation rate kdH was obtained as 2.73 × 10-4 s-1 (298 K) at pH 2.46. The dependence of kdH on the proton concentration (pH = 2.09-3.12) revealed a first-order dependence of kdH on [H+]; kdH = kd + k1[H+], where kd is the spontaneous dissociation rate and was 5.65 × 10-5 s-1, and k1 is the second-order rate constant and was 5.07 × 10-2 M-1 s-1. From the kd value, the half-life of the Try-Apr complex at physiological pH was determined as 3.4 h. The presence of the proton-assisted dissociation can be explained by the protonation of -COO- of the Asp residue in Try, which breaks the salt bridge with the -NH3+ group of Lys in Apr.
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Affiliation(s)
- Yumiko Sasaki
- Graduate School of Environmental Studies, Tohoku University, 6-6-07 Aramaki-Aoba, Aoba, Sendai, 980-8579, Japan
| | - Yosuke Sato
- Graduate School of Environmental Studies, Tohoku University, 6-6-07 Aramaki-Aoba, Aoba, Sendai, 980-8579, Japan
| | - Toru Takahashi
- Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
| | - Mitsuo Umetsu
- Graduate School of Engineering, Tohoku University, 6-6-11 Aramaki-Aoba, Aoba, Sendai, 980-8579, Japan
| | - Nobuhiko Iki
- Graduate School of Environmental Studies, Tohoku University, 6-6-07 Aramaki-Aoba, Aoba, Sendai, 980-8579, Japan.
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23
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Kim K, Subramaniyam S, Galaleldeen A, Nakazawa H, Umetsu M, Teizer W, Bhattacharyya S. Nanoparticle Assisted Remodeling of Proteotoxic SOD1 Mutants Alters the Biointerface of the Functional Interaction of Microtubules and Kinesin Motors. ACS Appl Bio Mater 2019; 2:4121-4128. [PMID: 35021426 DOI: 10.1021/acsabm.9b00501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transport deficits with motor neuron degeneration have been implicated in amyotrophic lateral sclerosis (ALS). We report a biomimetic system composed of microtubules/kinesin motor that mimics the dysregulated motor dynamics of ALS. Pathogenic ALS mutants A4V SOD1 completely shut off motility. Treatment with 5 nm citrate coated gold nanoparticles recovers the impaired motor stepping by remodeling the A4V SOD1 rather than stabilizing microtubules or protein folding. Instead, gold nanoparticles alter the protein by a mechanism that reforms protein elements of A4V SOD1, in turn fixing the aberrant interaction of kinesin with microtubules. Reinstating kinesin motility holds potential for managing debilitating ALS.
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Affiliation(s)
| | - Selvaraj Subramaniyam
- Department of Pharmaceutical Science and Chinese Traditional Medicine, Southwest University, Beibei, Chongqing 400715, China
| | - Ahmad Galaleldeen
- Department of Biological Science, St Mary's University, San Antonio, Texas 78228, United States
| | | | | | | | - Sanjib Bhattacharyya
- Department of Pharmaceutical Science and Chinese Traditional Medicine, Southwest University, Beibei, Chongqing 400715, China
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Holišová V, Konvičcková Z, Kratošová G, Kolenčcík M, Niide T, Umetsu M, Plachá D. Phytosynthesis of Au and Au/ZrO₂ bi-Phasic System Nanoparticles with Evaluation of Their Colloidal Stability. J Nanosci Nanotechnol 2019; 19:2807-2813. [PMID: 30501784 DOI: 10.1166/jnn.2019.15851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Due to its easy availability, preparation, handling and non-toxic nature, Equisetum arvense horsetail extract was chosen as a reducing, stabilizing and functionalizing agent for Au and bi-phasic Au/ZrO₂ nanoparticle phytosynthesis-inorganic nanoparticle synthesis mediated by plant extract. We studied Au and bi-phasic Au/ZrO₂ nanoparticles in colloids by various physical-chemical and analytical methods over 5 weeks. Dynamic Light Scattering and Scanning Transmission Electron Microscopy compared core and hydrodynamic diameters of nanoparticles. ζ-potential measurement indirectly determined nanoparticles stability in liquid medium. Ultraviolet-Visible Spectroscopy characterized basic absorbance maxima for both Au and the bi-phasic Au/ZrO₂ system. Finally, total metal concentration was determined using Inductively Coupled Plasma Mass Spectrometry. ζ-potential measurements proved satisfactory stability of both Au (-13.4 to -17 mV) and Au/ZrO₂ nanoparticles (-14.1 to -17.5 mV) over the experimental period. Scanning Transmission Electron Microscopy with Selected Area Diffraction analysis confirmed nanoparticles crystalline nature, and we determined 24 nm and 40 nm core nanogold diameters in Au and Au/ZrO₂ nanoparticle colloids. Dynamic light scattering analysis confirmed the dichotomy between particle sizes in liquid medium in the hundreds of nanometers measured, and long-term measurements confirmed reasonable colloid stability-a paramount parameter for potential nanoparticles applications; especially in heterogeneous catalysis.
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Affiliation(s)
- Veronika Holišová
- Nanotechnology Centre, VŠB - Technical University of Ostrava, 17. listopadu 15/2172, Ostrava 70833, Czech Republic
| | - Zuzana Konvičcková
- Nanotechnology Centre, VŠB - Technical University of Ostrava, 17. listopadu 15/2172, Ostrava 70833, Czech Republic
| | - Gabriela Kratošová
- Nanotechnology Centre, VŠB - Technical University of Ostrava, 17. listopadu 15/2172, Ostrava 70833, Czech Republic
| | - Marek Kolenčcík
- Department of Soil Science and Geology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia
| | - Teppei Niide
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11-606 Aoba, Aramaki, Aoba-ku, 980-8579 Sendai, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11-606 Aoba, Aramaki, Aoba-ku, 980-8579 Sendai, Japan
| | - Daniela Plachá
- Nanotechnology Centre, VŠB - Technical University of Ostrava, 17. listopadu 15/2172, Ostrava 70833, Czech Republic
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25
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Niide T, Manabe N, Nakazawa H, Akagi K, Hattori T, Kumagai I, Umetsu M. Complementary Design for Pairing between Two Types of Nanoparticles Mediated by a Bispecific Antibody: Bottom-Up Formation of Porous Materials from Nanoparticles. Langmuir 2019; 35:3067-3076. [PMID: 30689940 DOI: 10.1021/acs.langmuir.8b03687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Recent advances in biotechnology have enabled the generation of antibodies with high affinity for the surfaces of specific inorganic materials. Herein, we report the synthesis of functional materials from multiple nanomaterials by using a small bispecific antibody recombinantly constructed from gold-binding and ZnO-binding antibody fragments. The bispecific antibody-mediated spontaneous linkage of gold and ZnO nanoparticles forms a binary gold-ZnO nanoparticle composite membrane. The relatively low melting point of the gold nanoparticles and the solubility of ZnO in dilute acidic solution then allowed for the bottom-up synthesis of a nanoporous gold membrane by means of a low-energy, low-environmental-load protocol. The nanoporous gold membrane showed high catalytic activity for the reduction of p-nitrophenol to p-aminophenol by sodium borohydride. Here, we show the potential utility of nanoparticle pairing mediated by bispecific antibodies for the bottom-up construction of nanostructured materials from multiple nanomaterials.
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Affiliation(s)
- Teppei Niide
- Department of Biomolecular Engineering, Graduate School of Engineering , Tohoku University , Aoba 6-6-11, Aramaki , Aoba-ku, Sendai 980-8579 , Japan
| | - Noriyoshi Manabe
- Department of Biomolecular Engineering, Graduate School of Engineering , Tohoku University , Aoba 6-6-11, Aramaki , Aoba-ku, Sendai 980-8579 , Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering , Tohoku University , Aoba 6-6-11, Aramaki , Aoba-ku, Sendai 980-8579 , Japan
| | - Kazuto Akagi
- Advanced Institute for Materials Research , Tohoku University , 2-1-1 Katahira , Aoba-ku, Sendai 980-8577 , Japan
| | - Takamitsu Hattori
- Department of Biomolecular Engineering, Graduate School of Engineering , Tohoku University , Aoba 6-6-11, Aramaki , Aoba-ku, Sendai 980-8579 , Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering , Tohoku University , Aoba 6-6-11, Aramaki , Aoba-ku, Sendai 980-8579 , Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering , Tohoku University , Aoba 6-6-11, Aramaki , Aoba-ku, Sendai 980-8579 , Japan
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26
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Saito Y, Oikawa M, Nakazawa H, Niide T, Kameda T, Tsuda K, Umetsu M. Machine-Learning-Guided Mutagenesis for Directed Evolution of Fluorescent Proteins. ACS Synth Biol 2018; 7:2014-2022. [PMID: 30103599 DOI: 10.1021/acssynbio.8b00155] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Molecular evolution based on mutagenesis is widely used in protein engineering. However, optimal proteins are often difficult to obtain due to a large sequence space. Here, we propose a novel approach that combines molecular evolution with machine learning. In this approach, we conduct two rounds of mutagenesis where an initial library of protein variants is used to train a machine-learning model to guide mutagenesis for the second-round library. This enables us to prepare a small library suited for screening experiments with high enrichment of functional proteins. We demonstrated a proof-of-concept of our approach by altering the reference green fluorescent protein (GFP) so that its fluorescence is changed into yellow. We successfully obtained a number of proteins showing yellow fluorescence, 12 of which had longer wavelengths than the reference yellow fluorescent protein (YFP). These results show the potential of our approach as a powerful method for directed evolution of fluorescent proteins.
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Affiliation(s)
- Yutaka Saito
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Misaki Oikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Teppei Niide
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Koji Tsuda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
- Center for Advanced Intelligence Project, RIKEN, 1-4-1 Nihombashi, Chuo-ku, Tokyo 103-0027, Japan
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27
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Fujii H, Tanaka Y, Nakazawa H, Sugiyama A, Manabe N, Shinoda A, Shimizu N, Hattori T, Hosokawa K, Sujino T, Ito T, Niide T, Asano R, Kumagai I, Umetsu M. Compact Seahorse‐Shaped T Cell–Activating Antibody for Cancer Therapy. Adv Therap 2018. [DOI: 10.1002/adtp.201700031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hiroto Fujii
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences Tohoku University 2‐1‐1 Katahira Aoba‐ku Sendai 980–8577 Japan
- JST PRESTO 2‐1‐1 Katahira Aoba‐ku Sendai 980–8577 Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Aruto Sugiyama
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Noriyoshi Manabe
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Akira Shinoda
- Faculty of Advanced Life Science Hokkaido University Sapporo 060–0810 Japan
| | - Nobutaka Shimizu
- Photon Factory Institute of Materials Structure Science High Energy Accelerator Research Organization 1‐1 Oho Tsukuba Ibaraki 305–0801 Japan
| | - Takamitsu Hattori
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Katsuhiro Hosokawa
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Takuma Sujino
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Teppei Niide
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Ryutaro Asano
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Aoba 6‐6‐11 Aramaki Aoba‐ku Sendai 980–8579 Japan
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Kim K, Yoshinaga N, Bhattacharyya S, Nakazawa H, Umetsu M, Teizer W. Large-scale chirality in an active layer of microtubules and kinesin motor proteins. Soft Matter 2018; 14:3221-3231. [PMID: 29670958 DOI: 10.1039/c7sm02298k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
During the early developmental process of organisms, the formation of left-right laterality requires a subtle mechanism, as it is associated with other principal body axes. Any inherent chiral feature in an egg cell can in principal trigger this spontaneous breaking of chiral symmetry. Individual microtubules, major cytoskeletal filaments, are known as chiral objects. However, to date there lacks convincing evidence of a hierarchical connection of the molecular nature of microtubules to large-scale chirality, particularly at the length scale of an entire cell. Here we assemble an in vitro active layer, consisting of microtubules and kinesin motor proteins, on a glass surface. Upon inclusion of methyl cellulose, the layered system exhibits a long-range active nematic phase, characterized by the global alignment of gliding MTs. This nematic order spans over the entire system size in the millimeter range and, remarkably, allows hidden collective chirality to emerge as counterclockwise global rotation of the active MT layer. The analysis based on our theoretical model suggests that the emerging global nematic order results from the local alignment of MTs, stabilized by methyl cellulose. It also suggests that the global rotation arises from the MTs' intrinsic curvature, leading to preferential handedness. Given its flexibility, this layered in vitro cytoskeletal system enables the study of membranous protein behavior responsible for important cellular developmental processes.
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Affiliation(s)
- Kyongwan Kim
- WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai 980-8577, Japan
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29
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Sanada H, Kobayashi K, Oyama K, Maru T, Nakanishi T, Umetsu M, Asano R, Kumagai I. Affinity maturation of humanized anti-epidermal growth factor receptor antibody using a modified phage-based open sandwich selection method. Sci Rep 2018; 8:5414. [PMID: 29615700 PMCID: PMC5882652 DOI: 10.1038/s41598-018-23796-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/21/2018] [Indexed: 11/09/2022] Open
Abstract
Affinity maturation is one of the cardinal strategies for improving antibody function using in vitro evolutionary methods; one such well-established method is phage display. To minimise gene deletion, we previously developed an open sandwich (OS) method wherein selection was performed using only phage-displaying VH fragments after mixing with soluble VL fragments. The decrease in anti-EGFR antibody 528 affinity through humanization was successfully recovered by selecting VH mutants using this OS method. However, the affinity was not similar to that of parental 528. For further affinity maturation, we aimed to isolate VL mutants that act in synergy with VH mutants. However, the OS method could not be applied for selecting VL fragments because the preparation of soluble VH fragments was hampered by their instability and insolubility. Therefore, we initially designed a modified OS method based on domain-swapping of VH fragments, from added soluble Fv fragments to phage-displaying VL fragments. Using this novel Fv-added OS selection method, we successfully isolated VL mutants, and one of the Fv comprising VH and VL mutants showed affinity almost equivalent to that of parental 528. This method is applicable for engineering other VL fragments for affinity maturation.
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Affiliation(s)
- Hideaki Sanada
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Kazuki Kobayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Kenji Oyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Takamitsu Maru
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Takeshi Nakanishi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Ryutaro Asano
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan. .,Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo, 184-8588, Japan.
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, 980-8579, Japan.
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Sugiyama A, Umetsu M, Nakazawa H, Niide T, Asano R, Hattori T, Kumagai I. High-throughput cytotoxicity and antigen-binding assay for screening small bispecific antibodies without purification. J Biosci Bioeng 2018; 126:153-161. [PMID: 29548844 DOI: 10.1016/j.jbiosc.2018.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/01/2018] [Accepted: 02/11/2018] [Indexed: 12/12/2022]
Abstract
The cytotoxicity of T cell-recruiting antibodies with their potential to damage late-stage tumor masses is critically dependent on their structural and functional properties. Recently, we reported a semi-high-throughput process for screening highly cytotoxic small bispecific antibodies (i.e., diabodies). In the present study, we improved the high-throughput performance of this screening process by removing the protein purification stage and adding a stage for determining the concentrations of the diabodies in culture supernatant. The diabodies were constructed by using an Escherichia coli expression system, and each diabody contained tandemly arranged peptide tags at the C-terminus, which allowed the concentration of diabodies in the culture supernatant to be quantified by using a tag-sandwich enzyme-linked immunosorbent assay. When estimated diabody concentrations were used to determine the cytotoxicity of unpurified antibodies, results comparable to those of purified antibodies were obtained. In a surface plasmon resonance spectroscopy-based target-binding assay, contaminants in the culture supernatant prevented us from conducting a quantitative binding analysis; however, this approach did allow relative binding affinity to be determined, and the relative binding affinities of the unpurified diabodies were comparable to those of the purified antibodies. Thus, we present here an improved high-throughput process for the simultaneous screening and determination of the binding parameters of highly cytotoxic bispecific antibodies.
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Affiliation(s)
- Aruto Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Teppei Niide
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Ryutaro Asano
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Takamitsu Hattori
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
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31
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Konvičková Z, Holišová V, Kolenčík M, Niide T, Kratošová G, Umetsu M, Seidlerová J. Phytosynthesis of colloidal Ag-AgCl nanoparticles mediated by Tilia sp. leachate, evaluation of their behaviour in liquid phase and catalytic properties. Colloid Polym Sci 2018. [DOI: 10.1007/s00396-018-4290-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Asano R, Nagai K, Makabe K, Takahashi K, Kumagai T, Kawaguchi H, Ogata H, Arai K, Umetsu M, Kumagai I. Structural considerations for functional anti-EGFR × anti-CD3 bispecific diabodies in light of domain order and binding affinity. Oncotarget 2018; 9:13884-13893. [PMID: 29568402 PMCID: PMC5862623 DOI: 10.18632/oncotarget.24490] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 02/10/2018] [Indexed: 01/05/2023] Open
Abstract
We previously reported a functional humanized bispecific diabody (bsDb) that targeted EGFR and CD3 (hEx3-Db) and enhancement of its cytotoxicity by rearranging the domain order in the V domain. Here, we further dissected the effect of domain order in bsDbs on their cross-linking ability and binding kinetics to elucidate general rules regarding the design of functional bsDbs. Using Ex3-Db as a model system, we first classified the four possible domain orders as anti-parallel (where both chimeric single-chain components are variable heavy domain (VH)-variable light domain (VL) or VL-VH order) and parallel types (both chimeric single-chain components are mixed with VH-VL and VL-VH order). Although anti-parallel Ex3-Dbs could cross-link the soluble target antigens, their cross-linking ability between soluble targets had no correlation with their growth inhibitory effects. In contrast, the binding affinity of one of the two constructs with a parallel-arrangement V domain was particularly low, and structural modeling supported this phenomenon. Similar results were observed with E2x3-Dbs, in which the V region of the anti-EGFR antibody clone in hEx3 was replaced with that of another anti-EGFR clone. Only anti-parallel types showed affinity-dependent cancer inhibitory effects in each molecule, and E2x3-LH (both components in VL-VH order) showed the most intense anti-tumor activity in vitro and in vivo. Our results showed that, in addition to rearranging the domain order of bsDbs, increasing their binding affinity may be an ideal strategy for enhancing the cytotoxicity of anti-parallel constructs and that E2x3-LH is particularly attractive as a candidate next-generation anti-cancer drug.
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Affiliation(s)
- Ryutaro Asano
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan.,Present Address: Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Keisuke Nagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, Yonezawa 992-8510, Japan
| | - Kento Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Takashi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Hiroko Kawaguchi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Hiromi Ogata
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Kyoko Arai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
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Saito R, Saito Y, Nakazawa H, Hattori T, Kumagai I, Umetsu M, Makabe K. Impact in stability during sequential CDR grafting to construct camelid VHH antibodies against zinc oxide and gold. J Biochem 2018; 164:21-25. [DOI: 10.1093/jb/mvy016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 01/11/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ryota Saito
- Department of Biochemical Engineering, Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata 992-8510, Japan
| | - Yutaro Saito
- Department of Biochemical Engineering, Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata 992-8510, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aramaki-aza-aoba 6-6-11, Sendai, Mayagi 980-8579, Japan
| | - Takamitsu Hattori
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aramaki-aza-aoba 6-6-11, Sendai, Mayagi 980-8579, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aramaki-aza-aoba 6-6-11, Sendai, Mayagi 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aramaki-aza-aoba 6-6-11, Sendai, Mayagi 980-8579, Japan
| | - Koki Makabe
- Department of Biochemical Engineering, Graduate School of Science and Engineering, Yamagata University, Jyonan 4-3-16, Yonezawa, Yamagata 992-8510, Japan
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Nakazawa H, Seta Y, Hirose T, Masuda Y, Umetsu M. Use of a Phage-Display Method to Identify Peptides that Bind to a Tin Oxide Nanosheets. Protein Pept Lett 2017; 25:68-75. [PMID: 29210630 DOI: 10.2174/0929866525666171206114429] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/30/2017] [Accepted: 11/18/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nanosheets of SnO2 which an n-type semiconductor with a rutile-type crystalline structure are predominantly used as gas sensors. SnO2 nanosheets have a tetragonal crystal structure where growth along the c-axis is suppressed to form a sheet. The major exposed facets of SnO2 nanosheets have {110}, {101} and {211} crystal planes along the a-axis, with the reduced {110} surface having a particularly high surface energy. Identifying peptides that bind to specific crystal planes by using peptide phage-display approach will increase the potential applications of metal oxide nanomaterials by fusing proteins with desirable active sites to peptides that adsorb at high density on the major exposed crystal plane of nanosheets. It may be possible to construct highly sensitive biosensors. OBJECTIVES The main objective of the present study is to identify peptides that adsorb preferentially to a SnO2 nanosheet by using peptide-phage display approach. METHODS Four milligrams of SnO2 nanosheet were mixed with 1011 plaque-forming units of Ph.D.-12 Phage Display Peptide Library. Phage-bound nanosheet particles were washed 10 times with 1 mL of phosphatebuffered saline containing 0.5% Tween 20. Phages bound to the nanosheet were eluted with three different buffers: (1) high-salt buffer containing 2 M NaCl (pH 7.5); (2) acidic buffer containing 200 mM Gly-HCl (pH 2.2); and (3) high-phosphate-ion buffer containing 500 mM NaH2PO4 (pH 7.5). The eluted phages were subjected to four or five rounds of biopanning. At each round, individual plaques were picked from the plates, and the amino acid sequences of the peptides were identified by DNA sequencing. The identified SnO2-binding peptides labeled with fluorescein isothiocyanate were synthesized. Adsorption isotherms were constructed at peptide concentrations ranging from 0.25 to 2.0 µM with 4mg of nanomaterials. RESULTS We were determined the sequences of 11 clones with the high-salt buffer, 7 with the high-phosphateion buffers, and 6 with the acidic buffer and three peptides (SnO2BPn1, 2, and 3), two peptides (SnO2BPa1 and SnO2BPa2), and one peptide (SnO2BPp1) concentrated under each condition were selected respectively. All six selected peptides contained at least one histidine residue. In addition, the His-Asn-Leu (HNL) sequence was found in two of the peptides (SnO2BPa1 and SnO2BPa2). We constructed adsorption isotherms for the six selected peptides using 4mg of nanosheets. All six peptides were well adsorbed on the SnO2 nanosheet. The adsorption isotherms for SnO2 material with different structure revealed that SnO2BPn1, -2, and -3, and SnO2BPp1, preferentially bound to the spherical SnO2 nanoparticles. SnO2BPa2 preferentially bound to the SnO2 nanosheet, and SnO2BPa1 bound equally to both materials. This result suggested that SnO2BPa2 bound to a specific crystal plane of the nanosheet. The major exposed facet of the SnO2 crystal was the {110} plane, suggesting that SnO2BPa2 likely adsorbed on the {110} plane. SnO2BPn1, SnO2BPn2, SnO2BPn3, SnO2BPa1, and SnO2BPp1 also bound to the other metal oxides, in particular to ZrO2. At pH 7.5, peptides with a negative charge at pH 7.5 (pI 8.5-12) can bind to ZrO2 and SnO2, if the binding is mediated by electrostatic interactions. Thus, it is likely that these five peptides bind to metal oxides via electrostatic interactions. In contrast, SnO2BPa2 had a structurally specific affinity, binding more with the SnO2 nanosheet than with the spherical SnO2 nanoparticles or other metal oxides. CONCLUSION We identified six peptides that adsorbed on a SnO2 nanosheet. Five of the selected peptides bound preferentially to spherical SnO2 nanoparticles rather than to the SnO2 nanosheet. Whereas, SnO2BPa2 exhibited specifically binding to the SnO2 nanosheet. Our results suggest that crystal plane recognition and material recognition by these peptides are mediated via different, independent mechanisms.
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Affiliation(s)
- Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yasuko Seta
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Tatsuya Hirose
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Yoshitake Masuda
- National Institute of Advanced Industrial Science and Technology(AIST), Nagoya, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
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Sugiyama A, Umetsu M, Nakazawa H, Niide T, Onodera T, Hosokawa K, Hattori S, Asano R, Kumagai I. A semi high-throughput method for screening small bispecific antibodies with high cytotoxicity. Sci Rep 2017; 7:2862. [PMID: 28588218 PMCID: PMC5460266 DOI: 10.1038/s41598-017-03101-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 04/24/2017] [Indexed: 01/13/2023] Open
Abstract
Small bispecific antibodies that induce T-cell-mediated cytotoxicity have the potential to damage late-stage tumor masses to a clinically relevant degree, but their cytotoxicity is critically dependent on their structural and functional properties. Here, we constructed an optimized procedure for identifying highly cytotoxic antibodies from a variety of the T-cell-recruiting antibodies engineered from a series of antibodies against cancer antigens of epidermal growth factor receptor family and T-cell receptors. By developing and applying a set of rapid operations for expression vector construction and protein preparation, we screened the cytotoxicity of 104 small antibodies with diabody format and identified some with 103-times higher cytotoxicity than that of previously reported active diabody. The results demonstrate that cytotoxicity is enhanced by synergistic effects between the target, epitope, binding affinity, and the order of heavy-chain and light-chain variable domains. We demonstrate the importance of screening to determine the critical rules for highly cytotoxic antibodies.
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Affiliation(s)
- Aruto Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan.
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Teppei Niide
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Tomoko Onodera
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Katsuhiro Hosokawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Shuhei Hattori
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Ryutaro Asano
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai, 980-8579, Japan.
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Bhattacharyya S, Kim K, Nakazawa H, Umetsu M, Teizer W. Modulating the microtubule-tau interactions in biomotility systems by altering the chemical environment. Integr Biol (Camb) 2016; 8:1296-1300. [PMID: 27785513 DOI: 10.1039/c6ib00182c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Obstacles in microtubule mediated neuronal transport can trigger dementia. We use bio-motility assays, that simulate the neuron chemistry in axonopathy, to screen chemicals, that retain the microtubule dynamics in healthy neuronal activity. Tau protein inhibits microtubule activity and leads to oligomerization. Iron(iii) untangles, whereas mono-sodium-glutamate destabilizes the microtubule oligomer.
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Affiliation(s)
- S Bhattacharyya
- WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, Japan
| | - K Kim
- WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, Japan
| | - H Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - M Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - W Teizer
- WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, Japan and Department of Physics and Astronomy, Texas A&M University, College Station, TX, USA. and Materials Science and Engineering, Texas A&M University, College Station, TX, USA
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Shibuya Y, Haga N, Asano R, Nakazawa H, Hattori T, Takeda D, Sugiyama A, Kurotani R, Kumagai I, Umetsu M, Makabe K. Generation of camelid VHH bispecific constructs via in-cell intein-mediated protein trans-splicing. Protein Eng Des Sel 2016; 30:15-21. [PMID: 27881685 DOI: 10.1093/protein/gzw057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 10/13/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
Abstract
Production of various combinations of bispecific variable domain of heavy chain of heavy chain-only antibody (VHH) constructs to evaluate their therapeutic potential usually requires several gene-engineering steps. Here, we present an alternative method of creating bispecific VHH constructs in vivo through protein trans-splicing (PTS) reaction; this method may reduce the number of gene manipulation steps required. As a proof-of-concept, we constructed a bispecific antibody (bsAb) containing an anti-epidermal growth factor receptor VHH and anti-green fluorescent protein VHH, and we evaluated and confirmed its bispecificity. We also tested antibody labeling by fluorescent protein tagging using the PTS reaction. Compared with the conventional gene construction method, bsAb construction via PTS is a promising alternative approach for generating multiple bsAb combinations.
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Affiliation(s)
- Yuki Shibuya
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Natsuki Haga
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Ryutaro Asano
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 183-8538, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11-606 Aoba-yama, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Takamitsu Hattori
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11-606 Aoba-yama, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Daisuke Takeda
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Aruto Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11-606 Aoba-yama, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Reiko Kurotani
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11-606 Aoba-yama, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11-606 Aoba-yama, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Koki Makabe
- Graduate School of Science and Engineering, Yamagata University, 4-3-16 Jyonan, Yonezawa, Yamagata 992-8510, Japan
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Kim K, Sikora A, Nakazawa H, Umetsu M, Hwang W, Teizer W. Isomorphic coalescence of aster cores formed in vitro from microtubules and kinesin motors. Phys Biol 2016; 13:056002. [PMID: 27652512 DOI: 10.1088/1478-3975/13/5/056002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We report fluorescence microscopy studies of the formation of aster-like structures emerging from a cellular element-based active system and a novel analysis of the aster condensation. The system consists of rhodamine labeled microtubules which are dynamically coupled by functionalized kinesin motor proteins cross-linked via streptavidin-coated quantum dots (QDs). The aster-shaped objects contain core structures. The cores are aggregates of the QD-motor protein complexes, and result from the dynamic condensation of sub-clusters that are connected to each other randomly. The structural specificity of the aster core reflects a configuration of the initial connectivity between sub-clusters. Detailed image analysis allows us to extract a novel correlation between the condensation speed and the sub-cluster separation. The size of the core is scaled down during the condensation process, following a power law dependence on the distance between sub-clusters. The exponent of the power law is close to two, as expected from a geometric model. This single exponent common to all the contractile lines implies that there exists a time regime during which an isomorphic contraction of the aster core continues during the condensation process. We analyze the observed contraction by using a model system with potential applicability in a wide range of emergent phenomena in randomly coupled active networks, which are prevalent in the cellular environment.
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Affiliation(s)
- K Kim
- WPI-Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Japan
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Takahara M, Budinova GALG, Nakazawa H, Mori Y, Umetsu M, Kamiya N. Salt-Switchable Artificial Cellulase Regulated by a DNA Aptamer. Biomacromolecules 2016; 17:3356-3362. [PMID: 27602779 DOI: 10.1021/acs.biomac.6b01141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel artificial cellulase was developed by conjugating a DNA aptamer to an endoglucanase catalytic domain, thereby substituting the natural carbohydrate-binding module. Circular dichroism spectroscopy and adsorption isotherm showed the binding motif of cellulose-binding DNA aptamer (CelApt) was G-quadruplex and stem-loop structures stabilized in the presence of salts, and CelApt binding preferred the amorphous region of the solid cellulose. By introducing the revealed salt-switchable cellulose-binding nature of CelApt into a catalytic domain of a cellulase, we created CelApt-catalytic domain conjugate possessing both controllable adsorption on the solid substrates and equal enzymatic activity to the wild-type cellulase. Thus potential use of a responsive DNA aptamer for biocatalysis at a solid surface was demonstrated.
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Affiliation(s)
- Mari Takahara
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University , 744 Motooka, Fukuoka 819-0395, Japan
| | | | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , 6-6-116 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Yutaro Mori
- Biomass Engineering Program, RIKEN , 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , 6-6-116 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University , 744 Motooka, Fukuoka 819-0395, Japan.,Division of Biotechnology, Center for Future Chemistry, Kyushu University , 744 Motooka, Fukuoka 819-0395, Japan
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Nakayama M, Sasaki R, Ogino C, Tanaka T, Morita K, Umetsu M, Ohara S, Tan Z, Nishimura Y, Akasaka H, Sato K, Numako C, Takami S, Kondo A. Titanium peroxide nanoparticles enhanced cytotoxic effects of X-ray irradiation against pancreatic cancer model through reactive oxygen species generation in vitro and in vivo. Radiat Oncol 2016; 11:91. [PMID: 27386977 PMCID: PMC4936232 DOI: 10.1186/s13014-016-0666-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 07/02/2016] [Indexed: 12/20/2022] Open
Abstract
Background Biological applications of nanoparticles are rapidly increasing, which introduces new possibilities to improve the efficacy of radiotherapy. Here, we synthesized titanium peroxide nanoparticles (TiOxNPs) and investigated their efficacy as novel agents that can potently enhance the effects of radiation in the treatment of pancreatic cancer. Methods TiOxNPs and polyacrylic acid-modified TiOxNPs (PAA-TiOxNPs) were synthesized from anatase-type titanium dioxide nanoparticles (TiO2NPs). The size and morphology of the PAA-TiOxNPs was evaluated using transmission electron microscopy and dynamic light scattering. The crystalline structures of the TiO2NPs and PAA-TiOxNPs with and without X-ray irradiation were analyzed using X-ray absorption. The ability of TiOxNPs and PAA-TiOxNPs to produce reactive oxygen species in response to X-ray irradiation was evaluated in a cell-free system and confirmed by flow cytometric analysis in vitro. DNA damage after X-ray exposure with or without PAA-TiOxNPs was assessed by immunohistochemical analysis of γ-H2AX foci formation in vitro and in vivo. Cytotoxicity was evaluated by a colony forming assay in vitro. Xenografts were prepared using human pancreatic cancer MIAPaCa-2 cells and used to evaluate the inhibition of tumor growth caused by X-ray exposure, PAA-TiOxNPs, and the combination of the two. Results The core structures of the PAA-TiOxNPs were found to be of the anatase type. The TiOxNPs and PAA-TiOxNPs showed a distinct ability to produce hydroxyl radicals in response to X-ray irradiation in a dose- and concentration-dependent manner, whereas the TiO2NPs did not. At the highest concentration of TiOxNPs, the amount of hydroxyl radicals increased by >8.5-fold following treatment with 30 Gy of radiation. The absorption of PAA-TiOxNPs enhanced DNA damage and resulted in higher cytotoxicity in response to X-ray irradiation in vitro. The combination of the PAA-TiOxNPs and X-ray irradiation induced significantly stronger tumor growth inhibition compared to treatment with either PAA-TiOxNPs or X-ray alone (p < 0.05). No apparent toxicity or weight loss was observed for 43 days after irradiation. Conclusions TiOxNPs are potential agents for enhancing the effects of radiation on pancreatic cancer and act via hydroxyl radical production; owing to this ability, they can be used for pancreatic cancer therapy in the future. Electronic supplementary material The online version of this article (doi:10.1186/s13014-016-0666-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Masao Nakayama
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, 7-5-2 Kusunokicho, Chuouku, Kobe, Hyogo, 650-0017, Japan
| | - Ryohei Sasaki
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, 7-5-2 Kusunokicho, Chuouku, Kobe, Hyogo, 650-0017, Japan.
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkoudaicho, Nadaku, Kobe, Hyogo, 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkoudaicho, Nadaku, Kobe, Hyogo, 657-8501, Japan
| | - Kenta Morita
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkoudaicho, Nadaku, Kobe, Hyogo, 657-8501, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6 Aramaki, Aza, Aobaku, Sendai, Miyagi, 980-8579, Japan
| | - Satoshi Ohara
- Joining and Welding Research Institute, Osaka University, 11-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Zhenquan Tan
- Joining and Welding Research Institute, Osaka University, 11-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Yuya Nishimura
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkoudaicho, Nadaku, Kobe, Hyogo, 657-8501, Japan
| | - Hiroaki Akasaka
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, 7-5-2 Kusunokicho, Chuouku, Kobe, Hyogo, 650-0017, Japan
| | - Kazuyoshi Sato
- Division of Environmental Engineering Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjincho, Kiryu, Gunma, 376-8515, Japan
| | - Chiya Numako
- Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba, 263-8522, Japan
| | - Seiichi Takami
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, Miyagi, 980-8577, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkoudaicho, Nadaku, Kobe, Hyogo, 657-8501, Japan
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Asano R, Koyama N, Hagiwara Y, Masakari Y, Orimo R, Arai K, Ogata H, Furumoto S, Umetsu M, Kumagai I. Anti-EGFR scFv tetramer (tetrabody) with a stable monodisperse structure, strong anticancer effect, and a long in vivo half-life. FEBS Open Bio 2016; 6:594-602. [PMID: 27419062 PMCID: PMC4887975 DOI: 10.1002/2211-5463.12073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 11/07/2022] Open
Abstract
The development of single-chain variable fragments (scFvs) as therapeutic agents has the potential to reduce the high cost of antibody production, but the development process often impairs scFv functions such as binding affinity and pharmacokinetics. Multimerization is one strategy for recovering or enhancing these lost functions. Previously, we constructed several antiepidermal growth factor receptor (EGFR) scFv multimers by modifying linker length and domain order. Antitumor effects comparable with those of the currently approved anti-EGFR therapeutic antibodies were observed for scFv trimers. In the present study, we fractionated an anti-EGFR scFv tetramer from the intracellular soluble fraction of an Escherichia coli transformant. Compared with the trimer, the tetramer showed higher affinity, greater cancer cell growth inhibition, and prolonged blood retention time. Furthermore, the tetramer did not dissociate into the trimer or other smaller species during long-term storage (up to 33 weeks). Thus, our developed scFv tetramer is an attractive candidate next-generation anti-EGFR therapeutic antibody that can be produced via a low-cost bacterial expression system.
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Affiliation(s)
- Ryutaro Asano
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan; Present address: Department of Biotechnology and Life Science Graduate School of Engineering Tokyo University of Agriculture and Technology Tokyo 184-8588 Japan
| | - Noriaki Koyama
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan
| | - Yasuyo Hagiwara
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan
| | - Yosuke Masakari
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan
| | - Ryota Orimo
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan
| | - Kyoko Arai
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan
| | - Hiromi Ogata
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan
| | - Shozo Furumoto
- Department of Radiopharmaceutical Chemistry Graduate School of Pharmaceutical Sciences Tohoku University Sendai Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering Graduate School of Engineering Tohoku University Sendai Japan
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Kato Y, Ogasawara S, Oki H, Honma R, Takagi M, Fujii Y, Nakamura T, Saidoh N, Kanno H, Umetsu M, Kamata S, Kubo H, Yamada M, Sawa Y, Morita KI, Harada H, Suzuki H, Kaneko MK. Novel Monoclonal Antibody LpMab-17 Developed by CasMab Technology Distinguishes Human Podoplanin from Monkey Podoplanin. Monoclon Antib Immunodiagn Immunother 2016; 35:109-16. [DOI: 10.1089/mab.2015.0077] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Yukinari Kato
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Satoshi Ogasawara
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroharu Oki
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Orthopaedic Surgery, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Ryusuke Honma
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Orthopaedic Surgery, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Michiaki Takagi
- Department of Orthopaedic Surgery, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Yuki Fujii
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takuro Nakamura
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Noriko Saidoh
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hazuki Kanno
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Japan
| | - Satoshi Kamata
- Department of Advanced Preventive Medicine for Infectious Disease, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Thoracic Surgery, Institute of Development, Aging, and Cancer, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroshi Kubo
- Department of Advanced Preventive Medicine for Infectious Disease, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshihiko Sawa
- Department of Morphological Biology, Fukuoka Dental College, Fukuoka, Japan
| | - Kei-ichi Morita
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Harada
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyoshi Suzuki
- Department of Pathology and Laboratory Medicine, Sendai Medical Center, Sendai, Japan
| | - Mika Kato Kaneko
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, Sendai, Japan
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43
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Sikora A, Ramón-Azcón J, Sen M, Kim K, Nakazawa H, Umetsu M, Kumagai I, Shiku H, Matsue T, Teizer W. Microtubule guiding in a multi-walled carbon nanotube circuit. Biomed Microdevices 2016; 17:78. [PMID: 26162482 DOI: 10.1007/s10544-015-9978-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In nanotechnological devices, mass transport can be initiated by pressure driven flow, diffusion or by employing molecular motors. As the scale decreases, molecular motors can be helpful as they are not limited by increased viscous resistance. Moreover, molecular motors can move against diffusion gradients and are naturally fitted for nanoscale transportation. Among motor proteins, kinesin has particular potential for lab-on-a-chip applications. It can be used for sorting, concentrating or as a mechanical sensor. When bound to a surface, kinesin motors propel microtubules in random directions, depending on their landing orientation. In order to circumvent this complication, the microtubule motion should be confined or guided. To this end, dielectrophoretically aligned multi-walled-carbon nanotubes (MWCNT) can be employed as nanotracks. In order to control more precisely the spatial repartition of the MWCNTs, a screening method has been implemented and tested. Polygonal patterns have been fabricated with the aim of studying the guiding and the microtubule displacement between MWCNT segments. Microtubules are observed to transfer between MWCNT segments, a prerequisite for the guiding of microtubules in MWCNT circuit-based biodevices. The effect of the MWCNT organization (crenellated or hexagonal) on the MT travel distance has been investigated as well.
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Affiliation(s)
- Aurélien Sikora
- WPI Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan
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44
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Niide T, Ozawa K, Nakazawa H, Oliveira D, Kasai H, Onodera M, Asano R, Kumagai I, Umetsu M. Organic crystal-binding peptides: morphology control and one-pot formation of protein-displaying organic crystals. Nanoscale 2015; 7:20155-20163. [PMID: 26572746 DOI: 10.1039/c5nr06471f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Crystalline assemblies of fluorescent molecules have different functional properties than the constituent monomers, as well as unique optical characteristics that depend on the structure, size, and morphological homogeneity of the crystal particles. In this study, we selected peptides with affinity for the surface of perylene crystal particles by exposing a peptide-displaying phage library in aqueous solution to perylene crystals, eluting the surface-bound phages by means of acidic desorption or liquid-liquid extraction, and amplifying the obtained phages in Escherichia coli. One of the perylene-binding peptides, PeryBPb1: VQHNTKYSVVIR, selected by this biopanning procedure induced perylene molecules to form homogenous planar crystal nanoparticles by means of a poor solvent method, and fusion of the peptide to a fluorescent protein enabled one-pot formation of protein-immobilized crystalline nanoparticles. The nanoparticles were well-dispersed in aqueous solution, and Förster resonance energy transfer from the perylene crystals to the fluorescent protein was observed. Our results show that the crystal-binding peptide could be used for simultaneous control of perylene crystal morphology and dispersion and protein immobilization on the crystals.
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Affiliation(s)
- Teppei Niide
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan.
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45
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Sikora A, Canova FF, Kim K, Nakazawa H, Umetsu M, Kumagai I, Adschiri T, Hwang W, Teizer W. Behavior of Kinesin Driven Quantum Dots Trapped in a Microtubule Loop. ACS Nano 2015; 9:11003-11013. [PMID: 26426418 DOI: 10.1021/acsnano.5b04348] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We report the observation of kinesin driven quantum dots (QDs) trapped in a microtubule loop, allowing the investigation of moving QDs for a long time and an unprecedented long distance. The QD conjugates did not depart from our observational field of view, enabling the tracking of specific conjugates for more than 5 min. The unusually long run length and the periodicity caused by the loop track allow comparing and studying the trajectory of the kinesin driven QDs for more than 2 full laps, i.e., about 70 μm, enabling a statistical analysis of interactions of the same kinesin driven object with the same obstacle. The trajectories were extracted and analyzed from kymographs with a newly developed algorithm. Despite dispersion, several repetitive trajectory patterns can be identified. A method evaluating the similarity is introduced allowing a quantitative comparison between the trajectories. The velocity variations appear strongly correlated to the presence of obstacles. We discuss the reasons making this long continuous travel distances on the loop track possible.
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Affiliation(s)
- Aurélien Sikora
- WPI Advanced Institute for Materials Research, Tohoku University , 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Filippo Federici Canova
- WPI Advanced Institute for Materials Research, Tohoku University , 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Kyongwan Kim
- WPI Advanced Institute for Materials Research, Tohoku University , 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , Sendai 980-8579, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , Sendai 980-8579, Japan
| | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University , Sendai 980-8579, Japan
| | - Tadafumi Adschiri
- WPI Advanced Institute for Materials Research, Tohoku University , 2-1-1 Katahira, Sendai 980-8577, Japan
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University , College Station, Texas 77843-3120, United States
- School of Computational Sciences, Korea Institute for Advanced Study , Seoul 130-722, Korea
- Materials Science and Engineering, Texas A&M University , College Station, Texas 77843-3003, United States
| | - Winfried Teizer
- WPI Advanced Institute for Materials Research, Tohoku University , 2-1-1 Katahira, Sendai 980-8577, Japan
- Materials Science and Engineering, Texas A&M University , College Station, Texas 77843-3003, United States
- Department of Physics and Astronomy, Texas A&M University , College Station, Texas 77843-4242, United States
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Sasaki R, Kitazawa S, Kitahara R, Nakazawa H, Tanaka Y, Kumagai I, Umetsu M, Makabe K. Zinc Ion-binding Activity of an Anti-ZnO VHH Antibody, 4F2. CHEM LETT 2015. [DOI: 10.1246/cl.150537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ryosuke Sasaki
- Graduate School of Science and Engineering, Yamagata University
| | | | - Ryo Kitahara
- College of Pharmaceutical Sciences, Ritsumeikan University
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University
| | | | - Izumi Kumagai
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University
| | - Koki Makabe
- Graduate School of Science and Engineering, Yamagata University
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Nakayama M, Sasaki R, Mukohara T, Ogino C, Morita K, Umetsu M, Ohara S, Sato K, Numako C, Takami S, Kondo A. Abstract 3337: Titanium peroxide nanoparticles enhance antitumor efficacy through reactive oxygen species in pancreatic cancer radiation therapy. Tumour Biol 2015. [DOI: 10.1158/1538-7445.am2015-3337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Asano R, Shimomura I, Konno S, Ito A, Masakari Y, Orimo R, Taki S, Arai K, Ogata H, Okada M, Furumoto S, Onitsuka M, Omasa T, Hayashi H, Katayose Y, Unno M, Kudo T, Umetsu M, Kumagai I. Rearranging the domain order of a diabody-based IgG-like bispecific antibody enhances its antitumor activity and improves its degradation resistance and pharmacokinetics. MAbs 2014; 6:1243-54. [PMID: 25517309 PMCID: PMC4623410 DOI: 10.4161/mabs.29445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
One approach to creating more beneficial therapeutic antibodies is to develop bispecific antibodies (bsAbs), particularly IgG-like formats with tetravalency, which may provide several advantages such as multivalent binding to each target antigen. Although the effects of configuration and antibody-fragment type on the function of IgG-like bsAbs have been studied, there have been only a few detailed studies of the influence of the variable fragment domain order. Here, we prepared four types of hEx3-scDb-Fc, IgG-like bsAbs, built from a single-chain hEx3-Db (humanized bispecific diabody [bsDb] that targets epidermal growth factor receptor and CD3), to investigate the influence of domain order and fusion manner on the function of a bsDb with an Fc fusion format. Higher cytotoxicities were observed with hEx3-scDb-Fcs with a variable light domain (VL)-variable heavy domain (VH) order (hEx3-scDb-Fc-LHs) compared with a VH-VL order, indicating that differences in the Fc fusion manner do not affect bsDb activity. In addition, flow cytometry suggested that the higher cytotoxicities of hEx3-scDb-Fc-LH may be attributable to structural superiority in cross-linking. Interestingly, enhanced degradation resistance and prolonged in vivo half-life were also observed with hEx3-scDb-Fc-LH. hEx3-scDb-Fc-LH and its IgG2 variant exhibited intense in vivo antitumor effects, suggesting that Fc-mediated effector functions are dispensable for effective anti-tumor activities, which may cause fewer side effects. Our results show that merely rearranging the domain order of IgG-like bsAbs can enhance not only their antitumor activity, but also their degradation resistance and in vivo half-life, and that hEx3-scDb-Fc-LHs are potent candidates for next-generation therapeutic antibodies.
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Key Words
- ADCC, antibody-dependent cell-mediated cytotoxicity
- AUC, area-under-the-curve
- CD3
- EGFR, epidermal growth factor receptor
- FITC-CD3ϵγ, fluorescein isothiocyanate-labeled CD3ϵγ; DVD-IgTM, dual variable domain immunoglobulin
- FITC-sEGFR, FITC-labeled sEGFR
- Fv, variable fragment
- ICR, imprinting control region
- IgG-like bispecific antibody
- MTS, 3-(4, 5-dimethylthiazole-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt
- PBMCs, peripheral blood mononuclear cells
- PBS, phosphate-buffered saline
- SDS-PAGE, sodium dodecyl sulfate–polyacrylamide gel electrophoresis
- SPR, surface plasmon resonance
- SUV, standardized uptake value
- T-LAK cells, lymphokine-activated killer cells with the T-cell phenotype
- VH, variable heavy domain
- VL, variable light domain
- antibody engineering
- bispecific diabody
- bsAb, bispecific antibody
- bsDb, bispecific diabody
- cancer immunotherapy
- effective domain order
- epidermal growth factor receptor
- sEGFR, soluble EGFR
- scDb, single-chain diabody
- scFv, single-chain Fv
- taFv, tandem scFv
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Affiliation(s)
- Ryutaro Asano
- a Department of Biomolecular Engineering ; Graduate School of Engineering; Tohoku University ; Sendai , Japan
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Sikora A, Ramón-Azcón J, Kim K, Reaves K, Nakazawa H, Umetsu M, Kumagai I, Adschiri T, Shiku H, Matsue T, Hwang W, Teizer W. Molecular motor-powered shuttles along multi-walled carbon nanotube tracks. Nano Lett 2014; 14:876-881. [PMID: 24382007 DOI: 10.1021/nl4042388] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
As a complementary tool to nanofluidics, biomolecular-based transport is envisioned for nanotechnological devices. We report a new method for guiding microtubule shuttles on multi-walled carbon nanotube tracks, aligned by dielectrophoresis on a functionalized surface. In the absence of electric field and in fluid flow, alignment is maintained. The directed translocation of kinesin propelled microtubules has been investigated using fluorescence microscopy. To our knowledge, this is the first demonstration of microtubules gliding along carbon nanotubes.
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Affiliation(s)
- Aurélien Sikora
- WPI Advanced Institute for Materials Research, Tohoku University , 2-1-1 Katahira, Sendai, 980-8577, Japan
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50
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Tawa K, Umetsu M, Nakazawa H, Hattori T, Kumagai I. Application of 300× enhanced fluorescence on a plasmonic chip modified with a bispecific antibody to a sensitive immunosensor. ACS Appl Mater Interfaces 2013; 5:8628-8632. [PMID: 23945148 DOI: 10.1021/am402173y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The grating substrate covered with a metal layer, a plasmonic chip, and a bispecific antibody can play a key role in the sensitive detection of a marker protein with an immunosensor, because of the provision of an enhanced fluorescence signal and the preparation of a sensor surface densely modified with capture antibody, respectively. In this study, one of the tumor markers, a soluble epidermal growth factor receptor (sEGFR), was selected as the target to be detected. The ZnO- and silver-coated plasmonic chip with precise regularity and the appropriate duty ratio in the periodic structure further enhanced the fluorescence intensity. As for sensor surface modification with capture antibody, a bispecific antibody (anti-sEGFR and anti-ZnO antibody), the concentrated bispecific antibody solution was found to nonlinearly form a surface densely immobilized with antibody, because the binding process of a bispecific antibody to the ZnO surface can be a competitive process with adsorption of phosphate. As a result, the interface on the plasmonic chip provided a 300× enhanced fluorescence signal compared with that on a ZnO-coated glass slide, and therefore sEGFR was found to be quantitatively detected in a wide concentration range from 10 nM to 700 fM on our plasmonic surface.
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Affiliation(s)
- Keiko Tawa
- Health Research Institute, AIST , Ikeda, Osaka 563-8577, Japan
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