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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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Abstract
The new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the coronavirus disease 2019 (COVID-19) has significantly altered people's way of life. Despite widespread knowledge of vaccination, mask use, and avoidance of close contact, COVID-19 is still spreading around the world. Numerous research teams are examining the SARS-CoV-2 infection process to discover strategies to identify, prevent, and treat COVID-19 to limit the spread of this chronic coronavirus illness and restore lives to normalcy. Nanobodies have advantages over polyclonal and monoclonal antibodies (Ab) and Ab fragments, including reduced size, high stability, simplicity in manufacture, compatibility with genetic engineering methods, and lack of solubility and aggregation issues. Recent studies have shown that nanobodies that target the SARS-CoV-2 receptor-binding domain and disrupt ACE2 interactions are helpful in the prevention and treatment of SARS-CoV-2-infected animal models, despite the lack of evidence in human patients. The creation and evaluation of nanobodies, as well as their diagnostic and therapeutic applications against COVID-19, are discussed in this paper.
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Affiliation(s)
- Xuemei Feng
- Department
of Microbiology and Immunology, College
of Medicine and Health Science, China Three Gorges University, Yichang 443002, China
| | - Hu Wang
- Department
of Microbiology and Immunology, College
of Medicine and Health Science, China Three Gorges University, Yichang 443002, China
- Institute
of Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore 21215, United States
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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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Sun Y, Liu C, Zhong H, Wang C, Xu H, Chen W. Screening of autoantibodies as biomarkers in the serum of renal cancer patients based on human proteome microarray. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1909-1916. [PMID: 36789694 PMCID: PMC10157637 DOI: 10.3724/abbs.2022189] [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: 03/02/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022] Open
Abstract
The autoantibody in patients' serum can act as a biomarker for diagnosing cancer, and the differences in autoantibodies are significantly correlated with the changes in their target proteins. In this study, 16 renal cancer (RC) patients were assigned to the disease group, and 16 healthy people were assigned to the healthy control (HC) group. The human proteome microarray consisting of>19,500 proteins was used to examine the differences in IgG and IgM autoantibodies in sera between RC and HC. The comparative analysis of the microarray results shows that 101 types of IgG and 25 types of IgM autoantibodies are significantly higher in RC than in HC. Highly responsive autoantibodies can be candidate biomarkers (e.g., anti-KCNAB2 IgG and anti-RCN1 IgM). Extensive enzyme-linked immunosorbent assay (ELISA) was performed to screen sera in 72 RC patients and 66 healthy volunteers to verify the effectiveness of the new autoantibodies. The AUCs of anti-KCNAB2 IgG and anti-GAPDH IgG were 0.833 and 0.753, respectively. KCNAB2 achieves high protein expression, and its high mRNA level is confirmed to be an unfavorable prognostic marker in clear cell renal cell carcinoma (ccRCC) tissues. This study suggests that the high-throughput human proteome microarray can effectively screen autoantibodies in serum as candidate biomarkers, and their corresponding target proteins can lay a basis for the in-depth investigation into renal cancer.
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Affiliation(s)
- Yangyang Sun
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Department of Urology, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Chengxi Liu
- State Key Laboratory of Chemical Biology and Drug Discovery, Food Safety and Technology Research Centre and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Huidong Zhong
- Department of Medicinal ChemistryShantou University Medical CollegeShantou515041China
| | - Chenguang Wang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Haibo Xu
- Department of Urology, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Wei Chen
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Department of Urology, Shenzhen Second People’s Hospital, the First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
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Matys S, Morawietz L, Lederer F, Pollmann K. Characterization of the Binding Behavior of Specific Cobalt and Nickel Ion-Binding Peptides Identified by Phage Surface Display. SEPARATIONS 2022; 9:354. [DOI: 10.3390/separations9110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In recent years, the application focus of phage surface display (PSD) technology has been extended to the identification of metal ion-selective peptides. In previous studies, two phage clones—a nickel-binding one with the peptide motif CNAKHHPRCGGG and a cobalt-binding one with the peptide motif CTQMLGQLCGGG—were isolated, and their binding ability to metal-loaded NTA agarose beads was investigated. Here, the free cyclic peptides are characterized by UV/VIS spectroscopy with respect to their binding capacity for the respective target ion and in crossover experiments for the other ion by isothermal titration calorimetry (ITC) in different buffer systems. This revealed differences in selectivity and affinity. The cobalt-specific peptide is very sensitive to different buffers; it has a 20-fold higher affinity for cobalt and nickel under suitable conditions. The nickel-specific peptide binds more moderately and robustly in different buffers but only selectively to nickel.
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Qi H, Xue JB, Lai DY, Li A, Tao SC. Current advances in antibody-based serum biomarker studies: From protein microarray to phage display. Proteomics Clin Appl 2022; 16:e2100098. [PMID: 36071670 DOI: 10.1002/prca.202100098] [Citation(s) in RCA: 1] [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: 01/26/2022] [Revised: 08/16/2022] [Accepted: 09/05/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE This review aims to summarize the technological advances in the field of antibody-based biomarker studies by proteome microarray and phage display. In addition, the possible development directions of this field are also discussed. EXPERIMENTAL DESIGN We have focused on the antibody profiling by proteome microarray and phage display, including the technological advances, the tools/resources constructed, and the characteristics of both platforms. RESULTS With the help of tools/resources and technological advances in proteome microarray and phage display, the efficiency of profiling antibody-based biomarkers in serum samples has been greatly improved. CONCLUSIONS In the past few years, proteome microarray and phage display, especially the latter one, have already demonstrated their capacity and efficiency for biomarker identification. In the near future, we believe that more antibody-based biomarkers could be identified, and some of them could eventually be developed into real clinical applications.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Dan-Yun Lai
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ang Li
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
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