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Hsiao YC, Wallweber HA, Alberstein RG, Lin Z, Du C, Etxeberria A, Aung T, Shang Y, Seshasayee D, Seeger F, Watkins AM, Hansen DV, Bohlen CJ, Hsu PL, Hötzel I. Rapid affinity optimization of an anti-TREM2 clinical lead antibody by cross-lineage immune repertoire mining. Nat Commun 2024; 15:8382. [PMID: 39333507 PMCID: PMC11437124 DOI: 10.1038/s41467-024-52442-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/07/2024] [Indexed: 09/29/2024] Open
Abstract
We describe a process for rapid antibody affinity optimization by repertoire mining to identify clones across B cell clonal lineages based on convergent immune responses where antigen-specific clones with the same heavy (VH) and light chain germline segment pairs, or parallel lineages, bind a single epitope on the antigen. We use this convergence framework to mine unique and distinct VH lineages from rat anti-triggering receptor on myeloid cells 2 (TREM2) antibody repertoire datasets with high diversity in the third complementarity-determining loop region (CDR H3) to further affinity-optimize a high-affinity agonistic anti-TREM2 antibody while retaining critical functional properties. Structural analyses confirm a nearly identical binding mode of anti-TREM2 variants with subtle but significant structural differences in the binding interface. Parallel lineage repertoire mining is uniquely tailored to rationally explore the large CDR H3 sequence space in antibody repertoires and can be easily and generally applied to antibodies discovered in vivo.
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Affiliation(s)
- Yi-Chun Hsiao
- Department of Antibody Engineering, Genentech, South San Francisco, CA, 94080, USA
| | | | | | - Zhonghua Lin
- Department of Antibody Engineering, Genentech, South San Francisco, CA, 94080, USA
| | - Changchun Du
- Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | | | - Theint Aung
- Department of Antibody Engineering, Genentech, South San Francisco, CA, 94080, USA
| | - Yonglei Shang
- Department of Antibody Engineering, Genentech, South San Francisco, CA, 94080, USA
- Amberstone Biosciences, Irvine, CA, USA
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech, South San Francisco, CA, 94080, USA
| | - Franziska Seeger
- Prescient Design, a Genentech Accelerator, South San Francisco, CA, USA
| | - Andrew M Watkins
- Prescient Design, a Genentech Accelerator, South San Francisco, CA, USA
| | - David V Hansen
- Department of Neuroscience, Genentech, South San Francisco, CA, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | | | - Peter L Hsu
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Isidro Hötzel
- Department of Antibody Engineering, Genentech, South San Francisco, CA, 94080, USA.
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2
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Li Z, Jallow A, Nidiaye S, Huang Y, Zhang Q, Li P, Tang X. Improvement of the sensitivity of lateral flow systems for detecting mycotoxins: Up-to-date strategies and future perspectives. Compr Rev Food Sci Food Saf 2024; 23:e13255. [PMID: 38284606 DOI: 10.1111/1541-4337.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/05/2023] [Accepted: 09/30/2023] [Indexed: 01/30/2024]
Abstract
Mycotoxins are dangerous human and animal health-threatening secondary fungal metabolites that can be found in various food and agricultural products. Several countries have established regulations to restrict their presence in food and agricultural products destined for human and animal consumption. Consequently, the need to develop highly sensitive and smart detection systems was recognized worldwide. Lateral flow assay possesses the advantages of easy operation, rapidity, stability, accuracy, and specificity, and it plays an important role in the detection of mycotoxins. Nevertheless, strategies to comprehensively improve the sensitivity of lateral flow assay to mycotoxins in food have rarely been highlighted and discussed. In this article, a comprehensive overview was presented on the application of lateral flow assay in mycotoxin detection in food samples by highlighting the principle of lateral flow assay, presenting a detailed discussion on various analytical performance-improvement strategies, such as the development of high-affinity recognition reagents, immunogen immobilization methods, and signal amplification. Additionally, a detailed discussion on the various signal analyzers and interpretation approaches was provided. Finally, current hurdles and future perspectives on the application of lateral flow assay in the detection of mycotoxins were discussed.
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Affiliation(s)
- Zhiqiang Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oil seed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Abdoulie Jallow
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oil seed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Seyni Nidiaye
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oil seed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oil seed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qi Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oil seed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Food Safety Research Institute, HuBei University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Peiwu Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oil seed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Food Safety Research Institute, HuBei University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Xianghu Laboratory, Hangzhou, China
| | - Xiaoqian Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs; Laboratory of Risk Assessment for Oilseed Products (Wuhan), Ministry of Agriculture and Rural Affairs; Quality Inspection and Test Center for Oil seed Products, Ministry of Agriculture and Rural Affairs; Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Food Safety Research Institute, HuBei University, Wuhan, China
- Xianghu Laboratory, Hangzhou, China
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3
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Busato D, Capolla S, Durigutto P, Mossenta M, Bozzer S, Sblattero D, Macor P, Dal Bo M, Toffoli G. A novel complement-fixing IgM antibody targeting GPC1 as a useful immunotherapeutic strategy for the treatment of pancreatic ductal adenocarcinoma. J Transl Med 2023; 21:864. [PMID: 38017492 PMCID: PMC10685509 DOI: 10.1186/s12967-023-04745-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers with a very low survival rate at 5 years. The use of chemotherapeutic agents results in only modest prolongation of survival and is generally associated with the occurrence of toxicity effects. Antibody-based immunotherapy has been proposed for the treatment of PDAC, but its efficacy has so far proved limited. The proteoglycan glypican-1 (GPC1) may be a useful immunotherapeutic target because it is highly expressed on the surface of PDAC cells, whereas it is not expressed or is expressed at very low levels in benign neoplastic lesions, chronic pancreatitis, and normal adult tissues. Here, we developed and characterized a specific mouse IgM antibody (AT101) targeting GPC1. METHODS We developed a mouse monoclonal antibody of the IgM class directed against an epitope of GPC1 in close proximity to the cell membrane. For this purpose, a 46 amino acid long peptide of the C-terminal region was used to immunize mice by an in-vivo electroporation protocol followed by serum titer and hybridoma formation. RESULTS The ability of AT101 to bind the GPC1 protein was demonstrated by ELISA, and by flow cytometry and immunofluorescence analysis in the GPC1-expressing "PDAC-like" BXPC3 cell line. In-vivo experiments in the BXPC3 xenograft model showed that AT101 was able to bind GPC1 on the cell surface and accumulate in the BXPC3 tumor masses. Ex-vivo analyses of BXPC3 tumor masses showed that AT101 was able to recruit immunological effectors (complement system components, NK cells, macrophages) to the tumor site and damage PDAC tumor tissue. In-vivo treatment with AT101 reduced tumor growth and prolonged survival of mice with BXPC3 tumor (p < 0.0001). CONCLUSIONS These results indicate that AT101, an IgM specific for an epitope of GPC1 close to PDAC cell surface, is a promising immunotherapeutic agent for GPC1-expressing PDAC, being able to selectively activate the complement system and recruit effector cells in the tumor microenvironment, thus allowing to reduce tumor mass growth and improve survival in treated mice.
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Affiliation(s)
- Davide Busato
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Sara Capolla
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
| | - Paolo Durigutto
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Monica Mossenta
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Sara Bozzer
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
| | - Daniele Sblattero
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Paolo Macor
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Michele Dal Bo
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy.
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology, Centro Di Riferimento Oncologico (CRO) Di Aviano IRCCS, 33081, Aviano, Italy
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Spoendlin FC, Abanades B, Raybould MIJ, Wong WK, Georges G, Deane CM. Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope. Front Mol Biosci 2023; 10:1237621. [PMID: 37790877 PMCID: PMC10544996 DOI: 10.3389/fmolb.2023.1237621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/28/2023] [Indexed: 10/05/2023] Open
Abstract
The function of an antibody is intrinsically linked to the epitope it engages. Clonal clustering methods, based on sequence identity, are commonly used to group antibodies that will bind to the same epitope. However, such methods neglect the fact that antibodies with highly diverse sequences can exhibit similar binding site geometries and engage common epitopes. In a previous study, we described SPACE1, a method that structurally clustered antibodies in order to predict their epitopes. This methodology was limited by the inaccuracies and incomplete coverage of template-based modeling. In addition, it was only benchmarked at the level of domain-consistency on one virus class. Here, we present SPACE2, which uses the latest machine learning-based structure prediction technology combined with a novel clustering protocol, and benchmark it on binding data that have epitope-level resolution. On six diverse sets of antigen-specific antibodies, we demonstrate that SPACE2 accurately clusters antibodies that engage common epitopes and achieves far higher dataset coverage than clonal clustering and SPACE1. Furthermore, we show that the functionally consistent structural clusters identified by SPACE2 are even more diverse in sequence, genetic lineage, and species origin than those found by SPACE1. These results reiterate that structural data improve our ability to identify antibodies that bind to the same epitope, adding information to sequence-based methods, especially in datasets of antibodies from diverse sources. SPACE2 is openly available on GitHub (https://github.com/oxpig/SPACE2).
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Affiliation(s)
- Fabian C. Spoendlin
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Brennan Abanades
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Wing Ki Wong
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Large Molecule Research, Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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5
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Olsen TH, Abanades B, Moal IH, Deane CM. KA-Search, a method for rapid and exhaustive sequence identity search of known antibodies. Sci Rep 2023; 13:11612. [PMID: 37463925 DOI: 10.1038/s41598-023-38108-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Antibodies with similar amino acid sequences, especially across their complementarity-determining regions, often share properties. Finding that an antibody of interest has a similar sequence to naturally expressed antibodies in healthy or diseased repertoires is a powerful approach for the prediction of antibody properties, such as immunogenicity or antigen specificity. However, as the number of available antibody sequences is now in the billions and continuing to grow, repertoire mining for similar sequences has become increasingly computationally expensive. Existing approaches are limited by either being low-throughput, non-exhaustive, not antibody specific, or only searching against entire chain sequences. Therefore, there is a need for a specialized tool, optimized for a rapid and exhaustive search of any antibody region against all known antibodies, to better utilize the full breadth of available repertoire sequences. We introduce Known Antibody Search (KA-Search), a tool that allows for the rapid search of billions of antibody variable domains by amino acid sequence identity across either the variable domain, the complementarity-determining regions, or a user defined antibody region. We show KA-Search in operation on the [Formula: see text]2.4 billion antibody sequences available in the OAS database. KA-Search can be used to find the most similar sequences from OAS within 30 minutes and a representative subset of 10 million sequences in less than 9 seconds. We give examples of how KA-Search can be used to obtain new insights about an antibody of interest. KA-Search is freely available at https://github.com/oxpig/kasearch .
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Affiliation(s)
- Tobias H Olsen
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Brennan Abanades
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Iain H Moal
- GSK Medicines Research Centre, GlaxoSmithKline plc, Stevenage, SG1 2NY, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK.
- Exscientia plc, Oxford, OX4 4GE, UK.
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6
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Zhang Y, Li Q, Luo L, Duan C, Shen J, Wang Z. Application of germline antibody features to vaccine development, antibody discovery, antibody optimization and disease diagnosis. Biotechnol Adv 2023; 65:108143. [PMID: 37023966 DOI: 10.1016/j.biotechadv.2023.108143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Although the efficacy and commercial success of vaccines and therapeutic antibodies have been tremendous, designing and discovering new drug candidates remains a labor-, time- and cost-intensive endeavor with high risks. The main challenges of vaccine development are inducing a strong immune response in broad populations and providing effective prevention against a group of highly variable pathogens. Meanwhile, antibody discovery faces several great obstacles, especially the blindness in antibody screening and the unpredictability of the developability and druggability of antibody drugs. These challenges are largely due to poorly understanding of germline antibodies and the antibody responses to pathogen invasions. Thanks to the recent developments in high-throughput sequencing and structural biology, we have gained insight into the germline immunoglobulin (Ig) genes and germline antibodies and then the germline antibody features associated with antigens and disease manifestation. In this review, we firstly outline the broad associations between germline antibodies and antigens. Moreover, we comprehensively review the recent applications of antigen-specific germline antibody features, physicochemical properties-associated germline antibody features, and disease manifestation-associated germline antibody features on vaccine development, antibody discovery, antibody optimization, and disease diagnosis. Lastly, we discuss the bottlenecks and perspectives of current and potential applications of germline antibody features in the biotechnology field.
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Affiliation(s)
- Yingjie Zhang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Qing Li
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Liang Luo
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Changfei Duan
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China.
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7
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Brendza R, Gao X, Stark KL, Lin H, Lee SH, Hu C, Cai H, DiCara D, Hsiao YC, Ngu H, Foreman O, Baca M, Dohse M, Fortin JP, Corpuz R, Seshasayee D, Easton A, Ayalon G, Hötzel I, Chih B. Anti-α-synuclein c-terminal antibodies block PFF uptake and accumulation of phospho-synuclein in preclinical models of Parkinson's disease. Neurobiol Dis 2023; 177:105969. [PMID: 36535551 DOI: 10.1016/j.nbd.2022.105969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Parkinson's disease (PD), a neurodegenerative disease affecting dopaminergic (DA) neurons, is characterized by decline of motor function and cognition. Dopaminergic cell loss is associated with accumulation of toxic alpha synuclein aggregates. As DA neuron death occurs late in the disease, therapeutics that block the spread of alpha synuclein may offer functional benefit and delay disease progression. To test this hypothesis, we generated antibodies to the C terminal region of synuclein with high nanomolar affinity and characterized them in in vitro and in vivo models of spread. Interestingly, we found that only antibodies with high affinity to the distal most portion of the C-terminus robustly reduced uptake of alpha synuclein preformed fibrils (PFF) and accumulation of phospho (S129) alpha synuclein in cell culture. Additionally, the antibody treatment blocked the spread of phospho (S129) alpha synuclein associated-pathology in a mouse model of synucleinopathy. Blockade of neuronal PFF uptake by different antibodies was more predictive of in vivo activity than their binding potency to monomeric or oligomeric forms of alpha synuclein. These data demonstrate that antibodies directed to the C-terminus of the alpha synuclein have differential effects on target engagement and efficacy. Furthermore, our data provides additional support for the development of alpha synuclein antibodies as a therapeutic strategy for PD patients.
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Affiliation(s)
| | - Xiaoying Gao
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA
| | | | - Han Lin
- Neuroscience, Genentech, South San Francisco, CA, USA
| | - Seung-Hye Lee
- Neuroscience, Genentech, South San Francisco, CA, USA
| | - Changyun Hu
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Hao Cai
- Preclinical and Translational Pharmacokinetics, Genentech, South San Francisco, CA, USA
| | - Danielle DiCara
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Yi-Chun Hsiao
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Hai Ngu
- Pathology, Genentech, South San Francisco, CA, USA
| | - Oded Foreman
- Pathology, Genentech, South San Francisco, CA, USA
| | - Miriam Baca
- Pathology, Genentech, South San Francisco, CA, USA
| | - Monika Dohse
- Pathology, Genentech, South San Francisco, CA, USA
| | | | - Racquel Corpuz
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | | | - Amy Easton
- Neuroscience, Genentech, South San Francisco, CA, USA.
| | - Gai Ayalon
- Neuroscience, Genentech, South San Francisco, CA, USA
| | - Isidro Hötzel
- Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Ben Chih
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA.
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8
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Comeau SR, Thorsteinson N, Kumar S. Structural Considerations in Affinity Maturation of Antibody-Based Biotherapeutic Candidates. Methods Mol Biol 2023; 2552:309-321. [PMID: 36346600 DOI: 10.1007/978-1-0716-2609-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Affinity maturation is an important stage in biologic drug discovery as is the natural process of generating an immune response inside the human body. In this chapter, we describe in silico approaches to affinity maturation via a worked example. Both advantages and limitations of the computational methods used are critically examined. Furthermore, construction of affinity maturation libraries and how their outputs might be implemented in an experimental setting are also described. It should be noted that structure-based design of biologic drugs is an emerging field and the tools currently available require further development. Furthermore, there are no standardized structure-based strategies yet for antibody affinity maturation as this research relies heavily on scientific logic as well as creative intuition.
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Affiliation(s)
- Stephen R Comeau
- Computational Biochemistry and Bioinformatics Group, Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Nels Thorsteinson
- Scientific Services Manager, Biologics, Chemical Computing Group ULC, Montreal, QC, Canada
| | - Sandeep Kumar
- Computational Biochemistry and Bioinformatics Group, Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA.
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9
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Zhang C, Bzikadze AV, Safonova Y, Mirarab S. A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods. Front Immunol 2022; 13:1014439. [PMID: 36618367 PMCID: PMC9815712 DOI: 10.3389/fimmu.2022.1014439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Affinity maturation (AM) of B cells through somatic hypermutations (SHMs) enables the immune system to evolve to recognize diverse pathogens. The accumulation of SHMs leads to the formation of clonal lineages of antibody-secreting b cells that have evolved from a common naïve B cell. Advances in high-throughput sequencing have enabled deep scans of B cell receptor repertoires, paving the way for reconstructing clonal trees. However, it is not clear if clonal trees, which capture microevolutionary time scales, can be reconstructed using traditional phylogenetic reconstruction methods with adequate accuracy. In fact, several clonal tree reconstruction methods have been developed to fix supposed shortcomings of phylogenetic methods. Nevertheless, no consensus has been reached regarding the relative accuracy of these methods, partially because evaluation is challenging. Benchmarking the performance of existing methods and developing better methods would both benefit from realistic models of clonal lineage evolution specifically designed for emulating B cell evolution. In this paper, we propose a model for modeling B cell clonal lineage evolution and use this model to benchmark several existing clonal tree reconstruction methods. Our model, designed to be extensible, has several features: by evolving the clonal tree and sequences simultaneously, it allows modeling selective pressure due to changes in affinity binding; it enables scalable simulations of large numbers of cells; it enables several rounds of infection by an evolving pathogen; and, it models building of memory. In addition, we also suggest a set of metrics for comparing clonal trees and measuring their properties. Our results show that while maximum likelihood phylogenetic reconstruction methods can fail to capture key features of clonal tree expansion if applied naively, a simple post-processing of their results, where short branches are contracted, leads to inferences that are better than alternative methods.
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Affiliation(s)
- Chao Zhang
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, United States
| | - Andrey V. Bzikadze
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, United States
| | - Yana Safonova
- Computer Science and Engineering Department, University of California, San Diego, San Diego, CA, United States
| | - Siavash Mirarab
- Electrical and Computer Engineering Department, University of California, San Diego, San Diego, CA, United States
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10
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Wu H, Zhou Z, Xie S, Yan R, Gong M, Tian X, Wang Z. Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM. BMC Immunol 2022; 23:11. [PMID: 35246036 PMCID: PMC8895918 DOI: 10.1186/s12865-022-00482-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The B cell receptor (BCR) repertoire is highly diverse among individuals. Poor similarity of the spectrum among inbred baseline mice may limit the ability to discriminate true signals from those involving specific experimental factors. The repertoire similarity of the baseline status lacks intensive measurements. RESULTS We measured the repertoire similarity of IgH in blood and spleen samples from untreated BALB/c and C57BL/6J mice to investigate the baseline status of the two inbred strains. The antibody pool was stratified by the isotype of IgA, IgG and IgM. Between individuals, the results showed better convergence of CDR3 and clonal lineage profiles in IgM than in IgA and IgG, and better robustness of somatic mutation networks in IgM than in IgA and IgG. It also showed that the CDR3 clonotypes and clonal lineages shared better in the spleen samples than in the blood samples. The animal batch differences were detected in CDR3 evenness, mutated clonotype proportions, and maximal network degrees. A cut-off of 95% identity in the CDR3 nucleotide sequences was suitable for clonal lineage establishment. CONCLUSIONS Our findings reveal a natural landscape of BCR repertoire similarities between baseline mice and provide a solid reference for designing studies of mouse BCR repertoires.
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Affiliation(s)
- Hongkai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Shi Xie
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Yan
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingxing Gong
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
| | - Zhanhui Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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11
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Burman L, Chong YE, Duncan S, Klaus A, Rauch K, Hamel K, Hervé K, Pfaffen S, Collins DW, Heyries K, Nangle L, Hansen C, King DJ. Isolation of monoclonal antibodies from anti-synthetase syndrome patients and affinity maturation by recombination of independent somatic variants. MAbs 2021; 12:1836718. [PMID: 33131414 PMCID: PMC7646482 DOI: 10.1080/19420862.2020.1836718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The autoimmune disease known as Jo-1 positive anti-synthetase syndrome (ASS) is characterized by circulating antibody titers to histidyl-tRNA synthetase (HARS), which may play a role in modulating the non-canonical functions of HARS. Monoclonal antibodies to HARS were isolated by single-cell screening and sequencing from three Jo-1 positive ASS patients and shown to be of high affinity, covering diverse epitope space. The immune response was further characterized by repertoire sequencing from the most productive of the donor samples. In line with previous studies of autoimmune repertoires, these antibodies tended to have long complementarity-determining region H3 sequences with more positive-charged residues than average. Clones of interest were clustered into groups with related sequences, allowing us to observe different somatic mutations in related clones. We postulated that these had found alternate structural solutions for high affinity binding, but that mutations might be transferable between clones to further enhance binding affinity. Transfer of somatic mutations between antibodies within the same clonal group was able to enhance binding affinity in a number of cases, including beneficial transfer of a mutation from a lower affinity clone into one of higher affinity. Affinity enhancement was seen with mutation transfer both between related single-cell clones, and directly from related repertoire sequences. To our knowledge, this is the first demonstration of somatic hypermutation transfer from repertoire sequences to further mature in vivo derived antibodies, and represents an additional tool to aid in affinity maturation for the development of antibodies.
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Affiliation(s)
- Luke Burman
- Discovery Biology, aTyr Pharma , San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - Carl Hansen
- AbCellera Biologics Inc ., Vancouver, BC, USA
| | - David J King
- Discovery Biology, aTyr Pharma , San Diego, CA, USA
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12
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Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. Trace Reconstruction Problems in Computational Biology. IEEE TRANSACTIONS ON INFORMATION THEORY 2021; 67:3295-3314. [PMID: 34176957 PMCID: PMC8224466 DOI: 10.1109/tit.2020.3030569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction, practical solutions have only recently started to emerge in the context of two rapidly developing research areas: immunogenomics and DNA data storage. In immunogenomics, traces correspond to mutated copies of genes, with mutations generated naturally by the adaptive immune system. In DNA data storage, traces correspond to noisy copies of DNA molecules that encode digital data, with errors being artifacts of the data retrieval process. In this paper, we introduce several new trace generation models and open questions relevant to trace reconstruction for immunogenomics and DNA data storage, survey theoretical results on trace reconstruction, and highlight their connections to computational biology. Throughout, we discuss the applicability and shortcomings of known solutions and suggest future research directions.
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Affiliation(s)
- Vinnu Bhardwaj
- Electrical and Computer Engineering Department, University of California San Diego, La Jolla, USA
| | - Pavel A. Pevzner
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
| | - Cyrus Rashtchian
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
- Qualcomm Institute, University of California San Diego, La Jolla, USA
| | - Yana Safonova
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
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13
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Richardson E, Galson JD, Kellam P, Kelly DF, Smith SE, Palser A, Watson S, Deane CM. A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-pertussis toxoid antibodies. MAbs 2021; 13:1869406. [PMID: 33427589 PMCID: PMC7808390 DOI: 10.1080/19420862.2020.1869406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Due to their shared genetic history, antibodies from the same clonotype often bind to the same epitope. This knowledge is used in immune repertoire mining, where known binders are used to search bulk sequencing repertoires to identify new binders. However, current computational methods cannot identify epitope convergence between antibodies from different clonotypes, limiting the sequence diversity of antigen-specific antibodies that can be identified. We describe how the antibody binding site, the paratope, can be used to cluster antibodies with common antigen reactivity from different clonotypes. Our method, paratyping, uses the predicted paratope to identify these novel cross clonotype matches. We experimentally validated our predictions on a pertussis toxoid dataset. Our results show that even the simplest abstraction of the antibody binding site, using only the length of the loops involved and predicted binding residues, is sufficient to group antigen-specific antibodies and provide additional information to conventional clonotype analysis. Abbreviations: BCR: B-cell receptor; CDR: complementarity-determining region; PTx: pertussis toxoid
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Affiliation(s)
- Eve Richardson
- Department of Statistics, University of Oxford , Oxford, UK
| | - Jacob D Galson
- Alchemab Therapeutics Ltd , London, UK.,Division of Immunology, University Children's Hospital, University of Zurich, Zurich , Switzerland
| | - Paul Kellam
- Kymab Ltd , Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London , London, UK
| | - Dominic F Kelly
- Department of Paediatrics, University of Oxford , Oxford, UK.,Oxford University Hospitals NHS Foundation Trust , Oxford, UK
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14
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Goldstein LD, Chen YJJ, Wu J, Chaudhuri S, Hsiao YC, Schneider K, Hoi KH, Lin Z, Guerrero S, Jaiswal BS, Stinson J, Antony A, Pahuja KB, Seshasayee D, Modrusan Z, Hötzel I, Seshagiri S. Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies. Commun Biol 2019; 2:304. [PMID: 31428692 PMCID: PMC6689056 DOI: 10.1038/s42003-019-0551-y] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/15/2019] [Indexed: 01/24/2023] Open
Abstract
Obtaining full-length antibody heavy- and light-chain variable regions from individual B cells at scale remains a challenging problem. Here we use high-throughput single-cell B-cell receptor sequencing (scBCR-seq) to obtain accurately paired full-length variable regions in a massively parallel fashion. We sequenced more than 250,000 B cells from rat, mouse and human repertoires to characterize their lineages and expansion. In addition, we immunized rats with chicken ovalbumin and profiled antigen-reactive B cells from lymph nodes of immunized animals. The scBCR-seq data recovered 81% (n = 56/69) of B-cell lineages identified from hybridomas generated from the same set of B cells subjected to scBCR-seq. Importantly, scBCR-seq identified an additional 710 candidate lineages not recovered as hybridomas. We synthesized, expressed and tested 93 clones from the identified lineages and found that 99% (n = 92/93) of the clones were antigen-reactive. Our results establish scBCR-seq as a powerful tool for antibody discovery.
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Affiliation(s)
- Leonard D. Goldstein
- Molecular Biology, Genentech, South San Francisco, CA 94080 USA
- Bioinformatics & Computational Biology, Genentech, South San Francisco, CA 94080 USA
| | | | - Jia Wu
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | | | - Yi-Chun Hsiao
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Kellen Schneider
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Kam Hon Hoi
- Bioinformatics & Computational Biology, Genentech, South San Francisco, CA 94080 USA
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Zhonghua Lin
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Steve Guerrero
- Bioinformatics & Computational Biology, Genentech, South San Francisco, CA 94080 USA
| | | | - Jeremy Stinson
- Molecular Biology, Genentech, South San Francisco, CA 94080 USA
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Cochin, Kerala 682037 India
| | | | - Dhaya Seshasayee
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Zora Modrusan
- Molecular Biology, Genentech, South San Francisco, CA 94080 USA
| | - Isidro Hötzel
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Somasekar Seshagiri
- Molecular Biology, Genentech, South San Francisco, CA 94080 USA
- Present Address: SciGenom Research Foundation, Bangalore, 560099 India
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