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Liu X, Wang Y, Sun L, Xiao G, Hou N, Chen J, Wang W, Xu X, Gu Y. Screening and optimization of shark nanobodies against SARS-CoV-2 spike RBD. Antiviral Res 2024; 226:105898. [PMID: 38692413 DOI: 10.1016/j.antiviral.2024.105898] [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: 01/01/2024] [Revised: 03/28/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
SARS-CoV-2 continues to threaten human health, antibody therapy is one way to control the infection. Because new SARS-CoV-2 mutations are constantly emerging, there is an urgent need to develop broadly neutralizing antibodies to block the viral entry into host cells. VNAR from sharks is the smallest natural antigen binding domain, with the advantages of small size, flexible paratopes, good stability, and low manufacturing cost. Here, we used recombinant SARS-CoV-2 Spike-RBD to immunize sharks and constructed a VNAR phage display library. VNAR R1C2, selected from the library, efficiently binds to the RBD domain and blocks the infection of ACE2-positive cells by pseudovirus. Next, homologous bivalent VNARs were constructed through the tandem fusion of two R1C2 units, which enhanced both the affinity and neutralizing activity of R1C2. R1C2 was predicted to bind to a relatively conserved region within the RBD. By introducing mutations at four key binding sites within the CDR3 and HV2 regions of R1C2, the affinity and neutralizing activity of R1C2 were significantly improved. Furthermore, R1C2 also exhibits an effective capacity of binding to the Omicron variants (BA.2 and XBB.1). Together, these results suggest that R1C2 could serve as a valuable candidate for preventing and treating SARS-CoV-2 infections.
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Affiliation(s)
- Xiaochun Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, China
| | - Yanqing Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Lishan Sun
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Guokai Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ning Hou
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Jin Chen
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Wei Wang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Ximing Xu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Marine Biomedical Research Institute of Qingdao, Qingdao, 266071, China.
| | - Yuchao Gu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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2
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Wang Z, Xie X, He Z, Sun Z, Zhang Y, Mao F, Pei H, Zhang S, Hammock BD, Liu X. Development of Shark Single Domain Antibodies Specific for Human α-Fetoprotein and the Multimerization Strategy in Serum Detection. Anal Chem 2024; 96:4242-4250. [PMID: 38408370 DOI: 10.1021/acs.analchem.3c05675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Sensitive detection of cancer biomarkers can contribute to the timely diagnosis and treatment of diseases. In this study, the whitespotted bamboo sharks were immunized with human α-fetoprotein (AFP), and a phage-displayed variable new antigen receptor (VNAR) single domain antibody library was constructed. Then four unique VNARs (VNAR1, VNAR11, VNAR21, and VNAR25) against AFP were isolated from the library by biopanning for the first time. All of the sequences belong to type II of VNAR, and the VNAR11 was much different from the rest of the three sequences. Then VNAR1 and VNAR11 were selected to fuse with the C4-binding protein α chain (C4bpα) sequence and efficiently expressed in the Escherichia coli system. Furthermore, a VNAR-C4bpα-mediated sandwich chemiluminescence immunoassay (VSCLIA) was developed for the detection of AFP in human serum samples. After optimization, the VSCLIA showed a limit of detection of 0.74 ng/mL with good selectivity and accuracy. Moreover, the results of clinical serum samples detected by the VSCLIA were confirmed by an automatic immunoanalyzer in the hospital, indicating its practical application in actual samples. In conclusion, the novel antibody element VNAR exhibits great potential for immunodiagnosis, and this study also provides a new direction and experimental basis for AFP detection.
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Affiliation(s)
- Zheming Wang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Xiaoxia Xie
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Zhenyun He
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Zhichang Sun
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Yongli Zhang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Fujing Mao
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou 570311, China
| | - Sihang Zhang
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
| | - Bruce D Hammock
- Department of Entomology and Nematology, and UC Davis Comprehensive Cancer Center, University of California, Davis, California 95616, United States
| | - Xing Liu
- School of Food Science and Engineering, Hainan University, Haikou 570228, China
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3
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Zapata AG. The fish spleen. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109280. [PMID: 38086514 DOI: 10.1016/j.fsi.2023.109280] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/31/2023]
Abstract
In the present study, we review the structure and function of fish spleen with special emphasis on its condition in Elasmobranchs, Teleosts and Lungfish. Apart from the amount of splenic lymphoid tissue, the histological organization of the organ ensures the existence of areas involved in antigen trapping, the ellipsoids, and exhibit numerous melano-macrophages which appear isolated or forming the so-called melano-macrophage centres. An extensive discussion on the functional significance of these centres conclude that they are mere accumulations of macrophages consequence of tissue homeostasis rather than primitive germinal centres, as proposed by some authors.
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Affiliation(s)
- Agustín G Zapata
- Department of Cell Biology, Faculty of Biology, Complutense University, 28040, Madrid, Spain.
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4
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Malinge P, Chauchet X, Bourguignon J, Bosson N, Calloud S, Bautzova T, Borlet M, Laursen M, Kelpsas V, Rose N, Gueneau F, Ravn U, Magistrelli G, Fischer N. Structural analysis of light chain-driven bispecific antibodies targeting CD47 and PD-L1. MAbs 2024; 16:2362432. [PMID: 38849989 PMCID: PMC11164222 DOI: 10.1080/19420862.2024.2362432] [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: 02/16/2024] [Accepted: 05/28/2024] [Indexed: 06/09/2024] Open
Abstract
In contrast to natural antibodies that rely mainly on the heavy chain to establish contacts with their cognate antigen, we have developed a bispecific antibody format in which the light chain (LC) drives antigen binding and specificity. To better understand epitope-paratope interactions in this context, we determined the X-ray crystallographic structures of an antigen binding fragment (Fab) in complex with human CD47 and another Fab in complex with human PD-L1. These Fabs contain a κ-LC and a λ-LC, respectively, which are paired with an identical heavy chain (HC). The structural analysis of these complexes revealed the dominant contribution of the LCs to antigen binding, but also that the common HC provides some contacts in both CD47 and PD-L1 Fab complexes. The anti-CD47 Fab was affinity optimized by diversifying complementary-determining regions of the LC followed by phage display selections. Using homology modeling, the contributions of the amino acid modification to the affinity increase were analyzed. Our results demonstrate that, despite a less prominent role in natural antibodies, the LC can mediate high affinity binding to different antigens and neutralize their biological function. Importantly, Fabs containing a common variable heavy (VH) domain enable the generation of bispecific antibodies retaining a truly native structure, maximizing their therapeutic potential.
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Affiliation(s)
- Pauline Malinge
- Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland
| | - Xavier Chauchet
- Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland
| | | | - Nicolas Bosson
- Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland
| | | | - Tereza Bautzova
- Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland
| | - Marie Borlet
- Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland
| | | | | | | | - Franck Gueneau
- Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland
| | - Ulla Ravn
- Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland
| | | | - Nicolas Fischer
- Light Chain Bioscience - Novimmune SA, Plan-les-Ouates, Switzerland
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Lim HT, Kok BH, Leow CY, Leow CH. Exploring shark VNAR antibody against infectious diseases using phage display technology. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108986. [PMID: 37541634 DOI: 10.1016/j.fsi.2023.108986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Antibody with high affinity and specificity to antigen has widely used as a tool to combat various diseases. The variable domain of immunoglobulin new antigen receptor (VNAR) naturally found in shark contains autonomous function as single-domain antibody. Due to its excellent characteristics, the small, non-complex, and highly stable have made shark VNAR can acquires the antigen-binding capability that might not be reached by conventional antibody. Phage display technology enables shark VNAR to be presented on the surface of phage, allowing the exploration of shark VNAR as an alternative antibody format to target antigens from various infectious diseases. The application of phage-displayed shark VNAR in antibody library and biopanning eventually leads to the discovery and isolation of antigen-specific VNARs with diagnostic and therapeutic potential towards infectious diseases. This review provides an overview of the shark VNAR antibody, the types of phage display technology with comparison to the other types of display system, as well as the application and case studies of phage-displayed shark VNAR antibodies against infectious diseases.
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Affiliation(s)
- Hui Ting Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Boon Hui Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Gelugor, Penang, Malaysia.
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6
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Matz H, Dooley H. 450 million years in the making: mapping the evolutionary foundations of germinal centers. Front Immunol 2023; 14:1245704. [PMID: 37638014 PMCID: PMC10450919 DOI: 10.3389/fimmu.2023.1245704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023] Open
Abstract
Germinal centers (GCs) are distinct microanatomical structures that form in the secondary lymphoid organs of endothermic vertebrates (i.e., mammals and some birds). Within GCs, B cells undergo a Darwinian selection process to identify clones which can respond to pathogen insult as well as affinity mature the B cell repertoire. The GC response ultimately generates memory B cells and bone marrow plasma cells which facilitate humoral immunological memory, the basis for successful vaccination programs. GCs have not been observed in the secondary lymphoid organs of ectothermic jawed vertebrates (i.e., fishes, reptiles, and amphibians). However, abundant research over the past decades has indicated these organisms can produce antigen specific B cell responses and some degree of affinity maturation. This review examines data demonstrating that the fundamentals of B cell selection may be more conserved across vertebrate phylogeny than previously anticipated. Further, research in both conventional mammalian model systems and comparative models raises the question of what evolutionary benefit GCs provide endotherms if they are seemingly unnecessary for generating the basic functional components of jawed vertebrate humoral adaptive immune responses.
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Jeanne F, Bernay B, Sourdaine P. Comparative Proteome Analysis of Four Stages of Spermatogenesis in the Small-Spotted Catshark ( Scyliorhinus canicula), Using High-Resolution NanoLC-ESI-MS/MS. J Proteome Res 2023. [PMID: 37290099 DOI: 10.1021/acs.jproteome.3c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spermatogenesis is a highly specialized process of cell proliferation and differentiation leading to the production of spermatozoa from spermatogonial stem cells. Due to its testicular anatomy, Scyliorhinus canicula is an interesting model to explore stage-based changes in proteins during spermatogenesis. The proteomes of four testicular zones corresponding to the germinative niche and to spermatocysts (cysts) with spermatogonia (zone A), cysts with spermatocytes (zone B), cysts with young spermatids (zone C), and cysts with late spermatids (zone D) have been analyzed by nanoLC-ESI-MS/MS. Gene ontology and KEGG annotations were also performed. A total of 3346 multiple protein groups were identified. Zone-specific protein analyses highlighted RNA-processing, chromosome-related processes, cilium organization, and cilium activity in zones A, D, C, and D, respectively. Analyses of proteins with zone-dependent abundance revealed processes related to cellular stress, ubiquitin-dependent degradation by the proteasome, post-transcriptional regulation, and regulation of cellular homeostasis. Our results also suggest that the roles of some proteins, such as ceruloplasmin, optineurin, the pregnancy zone protein, PA28β or the Culling-RING ligase 5 complex, as well as some uncharacterized proteins, during spermatogenesis could be further explored. Finally, the study of this shark species allows one to integrate these data in an evolutionary context of the regulation of spermatogenesis. Mass spectrometry data are freely accessible via iProX-integrated Proteome resources (https://www.iprox.cn/) for reuse purposes.
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Affiliation(s)
- Fabian Jeanne
- Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR 8067, 14032 Caen cedex 5, France
| | - Benoît Bernay
- Université de Caen Normandie - Plateforme PROTEOGEN, US EMerode, 14032 Caen cedex 5, France
| | - Pascal Sourdaine
- Université de Caen Normandie, MNHN, SU, UA, CNRS, IRD, Laboratoire de Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), UMR 8067, 14032 Caen cedex 5, France
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8
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Pomarici ND, Cacciato R, Kokot J, Fernández-Quintero ML, Liedl KR. Evolution of the Immunoglobulin Isotypes-Variations of Biophysical Properties among Animal Classes. Biomolecules 2023; 13:801. [PMID: 37238671 PMCID: PMC10216798 DOI: 10.3390/biom13050801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/03/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
The adaptive immune system arose around 500 million years ago in jawed fish, and, since then, it has mediated the immune defense against pathogens in all vertebrates. Antibodies play a central role in the immune reaction, recognizing and attacking external invaders. During the evolutionary process, several immunoglobulin isotypes emerged, each having a characteristic structural organization and dedicated function. In this work, we investigate the evolution of the immunoglobulin isotypes, in order to highlight the relevant features that were preserved over time and the parts that, instead, mutated. The residues that are coupled in the evolution process are often involved in intra- or interdomain interactions, meaning that they are fundamental to maintaining the immunoglobulin fold and to ensuring interactions with other domains. The explosive growth of available sequences allows us to point out the evolutionary conserved residues and compare the biophysical properties among different animal classes and isotypes. Our study offers a general overview of the evolution of immunoglobulin isotypes and advances the knowledge of their characteristic biophysical properties, as a first step in guiding protein design from evolution.
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Affiliation(s)
| | | | | | - Monica L. Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Department of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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9
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Smith LC, Crow RS, Franchi N, Schrankel CS. The echinoid complement system inferred from genome sequence searches. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 140:104584. [PMID: 36343741 DOI: 10.1016/j.dci.2022.104584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
The vertebrate complement cascade is an essential host protection system that functions at the intersection of adaptive and innate immunity. However, it was originally assumed that complement was present only in vertebrates because it was activated by antibodies and functioned with adaptive immunity. Subsequently, the identification of the key component, SpC3, in sea urchins plus a wide range of other invertebrates significantly expanded the concepts of how complement functions. Because there are few reports on the echinoid complement system, an alternative approach to identify complement components in echinoderms is to search the deduced proteins encoded in the genomes. This approach identified known and putative members of the lectin and alternative activation pathways, but members of the terminal pathway are absent. Several types of complement receptors are encoded in the genomes. Complement regulatory proteins composed of complement control protein (CCP) modules are identified that may control the activation pathways and the convertases. Other regulatory proteins without CCP modules are also identified, however regulators of the terminal pathway are absent. The expansion of genes encoding proteins with Macpf domains is noteworthy because this domain is a signature of perforin and proteins in the terminal pathway. The results suggest that the major functions of the echinoid complement system are detection of foreign targets by the proteins that initiate the activation pathways resulting in opsonization by SpC3b fragments to augment phagocytosis and destruction of the foreign targets by the immune cells.
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Affiliation(s)
- L Courtney Smith
- Department of Biological Sciences, George Washington University, Washington DC, USA.
| | - Ryley S Crow
- Department of Biological Sciences, George Washington University, Washington DC, USA
| | - Nicola Franchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Catherine S Schrankel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, CA, USA
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10
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Cui Z, Zhao H, Chen X. Molecular and functional characterization of two IgM subclasses in large yellow croaker (Larimichthys crocea). FISH & SHELLFISH IMMUNOLOGY 2023; 134:108581. [PMID: 36754157 DOI: 10.1016/j.fsi.2023.108581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
As the predominant immunoglobulin (Ig) isotype, IgM plays a crucial role in the acquired immunity of vertebrates. There is only one Igμ gene in mammals, except cattle, while the number of Igμ gene varies among teleost fish. In the current study, we found two functional Igμ genes (Igμ1 and Igμ2) and a pseudo Cμ gene (ψIgμ) in large yellow croaker (Larimichthys crocea). Both Igμ1 and Igμ2 genes possessed two transcript variants, which encoded the heavy chains of secreted (sIgM1 and sIgM2) and membrane-bound IgM1 and IgM2 (mIgM1 and mIgM2), respectively. Both the heavy chains of sIgM1 and sIgM2 consisted of a variable Ig domain, four constant Ig domains (CH1, CH2, CH3 and CH4) and a secretory tail, while those of mIgM1 and mIgM2 consisted of a variable Ig domain, three constant Ig domains (CH1, CH2 and CH3), a transmembrane domain and a short cytoplasmic tail. Cysteine residues that are necessary for the formation of intrachain and interchain disulfide bonds and tryptophan residues that are important for the folding of the Ig superfamily domain were well conserved in large yellow croaker IgM1 and IgM2. Interestingly, large yellow croaker IgM2 had an extra cysteine (C94) in the CH1 domain compared with IgM1, which may cause the structural difference between IgM1 and IgM2. A liquid chromatography-tandem mass spectrometry analysis revealed that both IgM1 and IgM2 were present at the protein level in large yellow croaker serum. Both the Igμ1 and Igμ2 genes were mainly expressed in systemic immune tissues, such as head kidney and spleen, but the expression level of Igμ2 was much lower than that of Igμ1. After Pseudomonas plecoglossicida infection, the expression levels of Igμ1 and Igμ2 in both the spleen and head kidney were significantly upregulated, with a higher upregulation of Igμ2 than that of Igμ1. These results suggested that Igμ1 and Igμ2 may play a differential role in the immune response of large yellow croaker against bacterial infection.
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Affiliation(s)
- Zhengwei Cui
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Han Zhao
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinhua Chen
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Marine Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, 519000, China.
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11
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Shark nanobodies with potent SARS-CoV-2 neutralizing activity and broad sarbecovirus reactivity. Nat Commun 2023; 14:580. [PMID: 36737435 PMCID: PMC9896449 DOI: 10.1038/s41467-023-36106-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/13/2023] [Indexed: 02/05/2023] Open
Abstract
Despite rapid and ongoing vaccine and therapeutic development, SARS-CoV-2 continues to evolve and evade, presenting a need for next-generation diverse therapeutic modalities. Here we show that nurse sharks immunized with SARS-CoV-2 recombinant receptor binding domain (RBD), RBD-ferritin (RFN), or spike protein ferritin nanoparticle (SpFN) immunogens elicit a set of new antigen receptor antibody (IgNAR) molecules that target two non-overlapping conserved epitopes on the spike RBD. Representative shark antibody variable NAR-Fc chimeras (ShAbs) targeting either of the two epitopes mediate cell-effector functions, with high affinity to all SARS-CoV-2 viral variants of concern, including the divergent Omicron strains. The ShAbs potently cross-neutralize SARS-CoV-2 WA-1, Alpha, Beta, Delta, Omicron BA.1 and BA.5, and SARS-CoV-1 pseudoviruses, and confer protection against SARS-CoV-2 challenge in the K18-hACE2 transgenic mouse model. Structural definition of the RBD-ShAb01-ShAb02 complex enabled design and production of multi-specific nanobodies with enhanced neutralization capacity, and picomolar affinity to divergent sarbecovirus clade 1a, 1b and 2 RBD molecules. These shark nanobodies represent potent immunotherapeutics both for current use, and future sarbecovirus pandemic preparation.
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12
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Mirete-Bachiller S, Gambón-Deza F. Immunoglobulins genes in Neoceratodus forsteri and Protopterus annectens explain the origin of the immunoglobulins of the animals that passed ashore. Mol Immunol 2022; 152:97-105. [DOI: 10.1016/j.molimm.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/05/2022] [Accepted: 10/08/2022] [Indexed: 11/07/2022]
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13
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Liu C, Lin H, Cao L, Wang K, Sui J. Research progress on unique paratope structure, antigen binding modes, and systematic mutagenesis strategies of single-domain antibodies. Front Immunol 2022; 13:1059771. [PMID: 36479130 PMCID: PMC9720397 DOI: 10.3389/fimmu.2022.1059771] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/07/2022] [Indexed: 11/22/2022] Open
Abstract
Single-domain antibodies (sdAbs) showed the incredible advantages of small molecular weight, excellent affinity, specificity, and stability compared with traditional IgG antibodies, so their potential in binding hidden antigen epitopes and hazard detection in food, agricultural and veterinary fields were gradually explored. Moreover, its low immunogenicity, easy-to-carry target drugs, and penetration of the blood-brain barrier have made sdAbs remarkable achievements in medical treatment, toxin neutralization, and medical imaging. With the continuous development and maturity of modern molecular biology, protein analysis software and database with different algorithms, and next-generation sequencing technology, the unique paratope structure and different antigen binding modes of sdAbs compared with traditional IgG antibodies have aroused the broad interests of researchers with the increased related studies. However, the corresponding related summaries are lacking and needed. Different antigens, especially hapten antigens, show distinct binding modes with sdAbs. So, in this paper, the unique paratope structure of sdAbs, different antigen binding cases, and the current maturation strategy of sdAbs were classified and summarized. We hope this review lays a theoretical foundation to elucidate the antigen-binding mechanism of sdAbs and broaden the further application of sdAbs.
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14
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Hale M, Netland J, Chen Y, Thouvenel CD, Smith KN, Rich LM, Vanderwall ER, Miranda MC, Eggenberger J, Hao L, Watson MJ, Mundorff CC, Rodda LB, King NP, Guttman M, Gale M, Abraham J, Debley JS, Pepper M, Rawlings DJ. IgM antibodies derived from memory B cells are potent cross-variant neutralizers of SARS-CoV-2. J Exp Med 2022; 219:213384. [PMID: 35938988 PMCID: PMC9365875 DOI: 10.1084/jem.20220849] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/22/2022] [Accepted: 07/12/2022] [Indexed: 01/14/2023] Open
Abstract
Humoral immunity to SARS-CoV-2 can be supplemented with polyclonal sera from convalescent donors or an engineered monoclonal antibody (mAb) product. While pentameric IgM antibodies are responsible for much of convalescent sera's neutralizing capacity, all available mAbs are based on the monomeric IgG antibody subtype. We now show that IgM mAbs derived from immune memory B cell receptors are potent neutralizers of SARS-CoV-2. IgM mAbs outperformed clonally identical IgG antibodies across a range of affinities and SARS-CoV-2 receptor-binding domain epitopes. Strikingly, efficacy against SARS-CoV-2 viral variants was retained for IgM but not for clonally identical IgG. To investigate the biological role for IgM memory in SARS-CoV-2, we also generated IgM mAbs from antigen-experienced IgM+ memory B cells in convalescent donors, identifying a potent neutralizing antibody. Our results highlight the therapeutic potential of IgM mAbs and inform our understanding of the role for IgM memory against a rapidly mutating pathogen.
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Affiliation(s)
- Malika Hale
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Jason Netland
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Yu Chen
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | | | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | | | - Marcos C. Miranda
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Julie Eggenberger
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Linhui Hao
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Michael J. Watson
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | | | - Lauren B. Rodda
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA,Department of Biochemistry, University of Washington School of Medicine, Seattle, WA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA,Department of Immunology, University of Washington School of Medicine, Seattle, WA,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA,Correspondence to David J. Rawlings:
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15
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Wei L, Wang M, Xiang H, Jiang Y, Gong J, Su D, Al Azad MAR, Dong H, Feng L, Wu J, Chan LL, Yang N, Shi J. Bamboo Shark as a Small Animal Model for Single Domain Antibody Production. Front Bioeng Biotechnol 2021; 9:792111. [PMID: 34957081 PMCID: PMC8692893 DOI: 10.3389/fbioe.2021.792111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/08/2021] [Indexed: 01/08/2023] Open
Abstract
The development of shark single domain antibodies (sdAbs) is hindered by the high cost and tediousness of large-sized shark farming. Here, we demonstrated white-spotted bamboo sharks (Chiloscyllium plagiosum) being cultivated commercially as a promising small animal model to produce sdAbs. We found that immunoglobulin new antigen receptor (IgNAR) presented in bamboo shark genome, transcriptome, and plasma. Four complete IgNAR clusters including variable domains (vNARs) were discovered in the germline, and the Variable–Joining pair from IgNAR1 cluster was dominant from immune repertoires in blood. Bamboo sharks developed effective immune responses upon green fluorescent protein (GFP), near-infrared fluorescent protein iRFP713, and Freund’s adjuvant immunization revealed by elevated lymphocyte counts and antigen specific IgNAR. Before and after immunization, the complementarity determining region 3 (CDR3) of IgNAR were the major determinant of IgNAR diversity revealed by 400-bp deep sequencing. To prove that bamboo sharks could produce high-affinity IgNAR, we isolated anti-GFP and anti-iRFP713 vNARs with up to 0.3 and 3.8 nM affinities, respectively, from immunized sharks. Moreover, we constructed biparatopic vNARs with the highest known affinities (20.7 pM) to GFP and validated the functions of anti-GFP vNARs as intrabodies in mammalian cells. Taken together, our study will accelerate the discovery and development of bamboo shark sdAbs for biomedical industry at low cost and easy operation.
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Affiliation(s)
- Likun Wei
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Meiniang Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuan Jiang
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Jinhua Gong
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Dan Su
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - M A R Al Azad
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Hongming Dong
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Limin Feng
- Shen Zhen Research Institute, City University of Hong Kong, Shen Zhen, China
| | - Jiajun Wu
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Shen Zhen Research Institute, City University of Hong Kong, Shen Zhen, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Complete Genomics Inc., San Jose, CA, United States
| | - Jiahai Shi
- State Key Laboratory of Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Shen Zhen Research Institute, City University of Hong Kong, Shen Zhen, China.,Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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16
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Wan Z, Zhao Y, Sun Y. Immunoglobulin D and its encoding genes: An updated review. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 124:104198. [PMID: 34237381 DOI: 10.1016/j.dci.2021.104198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 04/03/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Since the identification of a functional Cδ gene in ostriches, immunoglobulin (Ig) D has been considered to be an extremely evolutionarily conserved Ig isotype besides the IgM found in all classes of jawed vertebrates. However, in contrast to IgM (which remains stable over evolutionary time), IgD shows considerable structural plasticity among vertebrate species and, moreover, its functions are far from elucidated even in humans and mice. Recently, several studies have shown that high expression of the IgD-B-cell receptor (IgD-BCR) may help physiologically autoreactive B cells survive in peripheral lymphoid tissues thanks to unresponsiveness to self-antigens and help their entry into germinal centers to "redeem" autoreactivity via somatic hypermutation. Other studies have demonstrated that secreted IgD may enhance mucosal homeostasis and immunity by linking B cells with basophils to optimize T-helper-2 cell-mediated responses and to constrain IgE-mediated basophil degranulation. Herein, we review the new discoveries on IgD-encoding genes in jawed vertebrates in the past decade. We also highlight advances in the functions of the IgD-BCR and secreted IgD in humans and mice.
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Affiliation(s)
- Zihui Wan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, Shandong, People's Republic of China.
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17
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Macela A, Kubelkova K. Why Does SARS-CoV-2 Infection Induce Autoantibody Production? Pathogens 2021; 10:380. [PMID: 33809954 PMCID: PMC8004127 DOI: 10.3390/pathogens10030380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 12/19/2022] Open
Abstract
SARS-CoV-2 infection induces the production of autoantibodies, which is significantly associated with complications during hospitalization and a more severe prognosis in COVID-19 patients. Such a response of the patient's immune system may reflect (1) the dysregulation of the immune response or (2) it may be an attempt to regulate itself in situations where the non-infectious self poses a greater threat than the infectious non-self. Of significance may be the primary virus-host cell interaction where the surface-bound ACE2 ectoenzyme plays a critical role. Here, we present a brief analysis of recent findings concerning the immune recognition of SARS-CoV-2, which, we believe, favors the second possibility as the underlying reason for the production of autoantibodies during COVID-19.
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Affiliation(s)
| | - Klara Kubelkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01 Hradec Kralove, Czech Republic;
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18
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Oreste U, Ametrano A, Coscia MR. On Origin and Evolution of the Antibody Molecule. BIOLOGY 2021; 10:biology10020140. [PMID: 33578914 PMCID: PMC7916673 DOI: 10.3390/biology10020140] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary Like many other molecules playing vital functions in animals, the antibody molecule possesses a complex structure with distinctive features. The structure of the basic unit, i.e., the immunoglobulin domain of very ancient origin is substantially simple. However, high complexity resides in the types and numbers of the domains composing the whole molecule. The emergence of the antibody molecule during evolution overturned the effectiveness of the organisms’ defense system. The particular organization of the coding genes, the mechanisms generating antibody diversity, and the plasticity of the overall protein structure, attest to an extraordinary successful evolutionary history. Here, we attempt to trace, across the evolutionary scale, the very early origins of the most significant features characterizing the structure of the antibody molecule and of the molecular mechanisms underlying its major role in recognizing an almost unlimited number of pathogens. Abstract The vertebrate immune system provides a powerful defense because of the ability to potentially recognize an unlimited number of pathogens. The antibody molecule, also termed immunoglobulin (Ig) is one of the major mediators of the immune response. It is built up from two types of Ig domains: the variable domain, which provides the capability to recognize and bind a potentially infinite range of foreign substances, and the constant domains, which exert the effector functions. In the last 20 years, advances in our understanding of the molecular mechanisms and structural features of antibody in mammals and in a variety of other organisms have uncovered the underlying principles and complexity of this fundamental molecule. One notable evolutionary topic is the origin and evolution of antibody. Many aspects have been clearly stated, but some others remain limited or obscure. By considering a wide range of prokaryotic and eukaryotic organisms through a literature survey about the topic, we have provided an integrated view of the emergence of antibodies in evolution and underlined the very ancient origins.
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Affiliation(s)
- Umberto Oreste
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
| | - Alessia Ametrano
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Maria Rosaria Coscia
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
- Correspondence: ; Tel.: +39-081-6132556
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