cDNA cloning of the immunoglobulin heavy chain genes in banded houndshark Triakis scyllium

Organ-specific repertoires of IgNAR gene in a cartilaginous fish

Cartilaginous fish possess one of the most ancient adaptive immune systems, and they uniquely produce the heavy chain-only antibody, immunoglobulin novel antigen receptor (IgNAR). In this study, we explored the mRNA transcription of genes related to antibody production and IgNAR diversity in various organs in banded houndsharks. IgNAR and antibody production-related genes exhibited similar relative transcription levels, with the highest expression detected in the spleen. Subsequently, we examined the diversity of IgNAR using next-generation sequencing. The most frequent clones were dominant (25 %-40 %) in the epigonal organ and liver but less common in the spleen. Large individual variation was noted in the kidney and pancreas. The length of complementarity-determining region 3 ranged 2-39 amino acids. The region tended to have a narrow length distribution of approximately 13 amino acids in the epigonal organ and liver, whereas wider length variation was noted in the kidney, pancreas, and spleen. Type II IgNAR variable regions (VNARs) were predominant (60 %-96 %) in all organs, whereas Type IV and "other" not conventionally defined VNARs were present at low frequencies and in different proportion between organs. Type I VNARs were present in multiple organs. The VNAR sequences were commonly shared among the epigonal organ, liver, and/or pancreas, but few were shared in the kidney or spleen.

The unexpected role of nurse shark pancreas as a secondary lymphoid organ

Secondary lymphoid organs (SLOs) provide a structured environment to facilitate interactions between low frequency antigen-specific B and T cells as well as cognate antigen displayed by antigen presenting cells (APCs), resulting in the initiation of effective adaptive immune responses. The spleen is the most evolutionary ancient SLO, emerging concurrently with adaptive immunity in an early jawed vertebrate ancestor. In mammals, the immunoprotective role of the spleen is complemented by that of other SLOs, notably a network of draining lymph nodes and gut-associated lymphoid tissue (GALT) to screen for infections throughout the host. However, lymph nodes are only present in endothermic vertebrates (ie, mammals and possibly some birds), so it is unclear how the majority of jawed vertebrate species maintain robust immune surveillance of their entire body to produce timely and efficacious antibody responses. While investigating adaptive immune responses in the nurse shark, a cartilaginous fish (Chondrichthyes) which last shared a common ancestor with other vertebrates ∼450 million yr ago, we discovered that the pancreas contains B cell follicles which are spatially distinct from the exocrine and endocrine pancreas. Furthermore, these "pancreatic B cell follicles" exhibit many of the hallmarks of B cell selection previously identified in the nurse shark spleen. Our results also demonstrate that antigen-specific antibodies are produced within the pancreas following immunization. Our study supports the designation of shark pancreas as a SLO and provides insight into how adaptive immune surveillance may function in the absence of lymph nodes.

Shark immune system: A review about their immunoglobulin repertoire

In the past few decades, the literature about the immune system of vertebrates has increased thanks to the research about new therapies and new biomolecules able to treat or eradicate many human autoimmune diseases. Researchers found that immunoglobulins (Igs) are the most versatile biomolecules able to recognize almost every existing epitope with their binding domains. Phylogenetically, the most recent vertebrates exhibit the greatest sequence diversification in their Igs to extend their ability to distinguish different antigens. Among cartilaginous fishes, the most ancient vertebrates on phylogenetic history, sharks possess four types of Igs with similar pathways to extend sequence diversity and binding domains variability. Their Ig new antigen receptor (IgNAR) represents one of the most versatile and small Ig type upon all other species. The shark species are fundamental sources of new therapeutic receptors lending a further step to treatments against several human diseases. The aim of this review is to analyze sharks Igs, focusing on IgNARs for each species.

The Janus (dual) model of immunoglobulin isotype evolution: Conservation and plasticity are the defining paradigms

The study of antibodies in jawed vertebrates (gnathostomes) provides every immunologist with a bird's eye view of how human immunoglobulins (Igs) came into existence and subsequently evolved into their present forms. It is a fascinating Darwinian history of conservation on the one hand and flexibility on the other, exemplified by the Ig heavy chain (H) isotypes IgM and IgD/W, respectively. The cartilaginous fish (e.g., sharks) Igs provide a glimpse of "how everything got off the ground," while the amphibians (e.g., the model Xenopus) reveal how the adaptive immune system made an about face with the emergence of Ig isotype switching and IgG-like structure/function. The evolution of mucosal Igs is a captivating account of malleability, convergence, and conservation, and a call to arms for future study! In between there are spellbinding chronicles of antibody evolution in each class of vertebrates and rather incredible stories of how antibodies can adapt to occupy niches, for example, single-domain variable regions, cold-adapted Igs, convergent mechanisms to dampen antibody function, provision of mucosal defense, and many more. The purpose here is not to provide an encyclopedic examination of antibody evolution, but rather to hit the high points and entice readers to appreciate how things "came to be."

A novel liver-specific immunoglobulin heavy chain-like gene in a cartilaginous fish

We identified a novel immunoglobulin (Ig) heavy chain-like gene (tsIgH) expressed in the liver of the banded houndshark Triakis scyllium by preliminary transcriptomic analysis. The tsIgH gene showed less than 30% of amino acid identities to Ig genes of the shark. The gene encodes one variable domain (VH) and three conserved domains (CH1-CH3) with a predicted signal peptide. Interestingly, this protein has only one cysteine residue in a linker region between VH and CH1 other than those required for the formation of the immunoglobulin domain. Genome sequencing revealed that each of the domains was encoded by a corresponding single exon, and the exon-intron structures of the homologues are conserved in the other cartilaginous fishes. By RT-qPCR analysis, the transcript of the tsIgH gene was observed only in the liver, while that of the IgM was mainly detected in the epigonal organ, liver, and spleen. The novel Ig-heavy chain-like gene in cartilaginous fish may provide new clues to the evolution of immunoglobulin genes.

Mass Spectrometry Analysis of Shark Skin Proteins

The mucus layer covering the skin of fish has several roles, including protection against pathogens and mechanical damage in which proteins play a key role. While proteins in the skin mucus layer of various common bony fish species have been explored, the proteins of shark skin mucus remain unexplored. In this pilot study, we examine the protein composition of the skin mucus in spiny dogfish sharks and chain catsharks through mass spectrometry (NanoLC-MS/MS). Overall, we identified 206 and 72 proteins in spiny dogfish (Squalus acanthias) and chain catsharks (Scyliorhinus retifer), respectively. Categorization showed that the proteins belonged to diverse biological processes and that most proteins were cellular albeit a significant minority were secreted, indicative of mucosal immune roles. The secreted proteins are reviewed in detail with emphasis on their immune potentials. Moreover, STRING protein-protein association network analysis showed that proteins of closely related shark species were more similar as compared to a more distantly related shark and a bony fish, although there were also significant overlaps. This study contributes to the growing field of molecular shark studies and provides a foundation for further research into the functional roles and potential human biomedical implications of shark skin mucus proteins.

Novel Approach for Obtaining Variable Domain of New Antigen Receptor with Different Physicochemical Properties from Japanese Topeshark (Hemitriakis japanica)

Diverse candidate antibodies are needed to successfully identify therapeutic and diagnostic applications. The variable domain of IgNAR (VNAR), a shark single-domain antibody, has attracted attention owing to its favorable physicochemical properties. The phage display method used to screen for optimal VNARs loses sequence diversity because of the bias caused by the differential ease of protein expression in Escherichia coli. Here, we investigated a VNAR selection method that combined panning with various selection pressures and next-generation sequencing (NGS) analyses to obtain additional candidates. Drawing inspiration from the physiological conditions of sharks and the physicochemical properties of VNARs, we examined the effects of NaCl and urea concentrations, low temperature, and preheating at the binding step of panning. VNAR phage libraries generated from Japanese topeshark (Hemitriakis japanica) were enriched under these conditions. We then performed NGS analysis and attempted to select clones that were specifically enriched under each panning condition. The identified VNARs exhibited higher reactivity than those obtained by panning without selection pressure. Additionally, they possess physicochemical properties that reflect their respective selection pressures. These results can greatly enhance our understanding of VNAR properties and offer guidance for the screening of high-quality VNAR clones that are present at low frequencies.

Isolation and characterization of single domain antibodies from banded houndshark (Triakis scyllium) targeting SARS-CoV-2 spike RBD protein

The COVID-19 pandemic has significantly impacted human health for three years. To mitigate the spread of SARS-CoV-2, the development of neutralizing antibodies has been accelerated, including the exploration of alternative antibody formats such as single-domain antibodies. In this study, we identified new variable antigen receptors (VNARs) specific for the receptor binding domain (RBD) of SARS-CoV-2 by immunizing a banded houndshark (Triakis scyllium) with recombinant wild-type RBD. Notably, the CoV₂NAR-1 clone showed high binding affinities in the nanomolar range to various RBDs and demonstrated neutralizing activity against SARS-CoV-2 pseudoviruses. These results highlight the potential of the banded houndshark as an animal model for the development of VNAR-based therapeutics or diagnostics against future pandemics.

IgNAR antibody: Structural features, diversity and applications

In response to the invasion of exogenous microorganisms, one of the defence strategies of the immune system is to produce antibodies. Cartilaginous fish is among those who evolved the earliest humoral immune system that utilizes immunoglobulin-type antibodies. The cartilaginous fish antibodies fall into three categories: IgW, IgM, and IgNAR. The shark Immunoglobulin Novel Antigen Receptor (IgNAR) constitutes disulfide-bonded dimers of two protein chains, similar to the heavy chain of mammalian IgGs. Shark IgNAR is the primary antibody of a shark's adaptive immune system with a serum concentration of 0.1-1.0 mg/mL. Its structure comprises of one variable (V) domain (VNAR) and five constant (C1 -C5) domains in the secretory form. VNARs are classified into several subclasses based on specific properties such as the quantity and position of additional non-canonical cysteine (Cys) residues in the VNAR. The VDJ recombination in IgNAR comprises various fragments; one variable component, three diverse sections, one joining portion, and a solitary arrangement of constant fragments framed in each IgNAR gene cluster. The re-arrangement happens just inside this gene cluster bringing about a VD1D2D3J segment. Therefore, four re-arrangement procedures create the entire VNAR space. IgNAR antibody can serve as an excellent diagnostic, therapeutic, and research tool because it has a smaller size, high specificity for antigen-binding, and perfect stability. The domain characterization, structural features, types, diversity and therapeutic applications of IgNAR molecules are highlighted in this review. It would be helpful for further research on IgNAR antibodies acting as an essential constituent of the adaptive immune system and a potential therapeutic agent.

Preliminary characterization of pathogen-detection activities of serum antibodies from the banded houndshark Triakis scyllium

Antibodies of cartilaginous fish are of scientific interest due to their phylogenetic position. In the present study, we developed antiserum against IgM of the banded houndshark, Triakis scyllium, and characterized binding activity of the IgM against fish pathogenic bacteria. Pentameric and monomeric IgM antibodies were separated by gel filtration chromatography using high performance liquid chromatography and SDS-PAGE. Antisera were developed by immunizing rabbits with unfractionated IgM antibodies separated by SDS-PAGE electrophoresis. Shark serum antibodies were found to have binding affinity for Aeromonas hydrophila, Vibrio anguillarum, Edwardsiella tarda, and Pseudomonas plecoglossicida antigens but not Lactococcus garvieae by enzyme-linked immunosorbent assay. We speculate the binding activities of shark antibodies may confer protection against certain bacterial pathogens.

Sequence structure character of IgNAR Sec in whitespotted bamboo shark (Chiloscyllium plagiosum)

Whitespotted bamboo shark (Chiloscyllium plagiosum) is a demersal cartilaginous fish with an adaptive immune system founded upon immunoglobulins. In this manuscript, we characterize the IgNAR of the whitespotted bamboo shark. A newly discovered alternative splicing form of IgNAR Sec (IgNAR_short (ΔC2-C3) Sec) was identified, in which the C1 domain was spliced directly to the C4 domain, the process resulted in a molecule containing three constant domains. However, a single unpaired cysteine remains in the highly flexible hinge region, contributing in the formation of an interchain disulfide bond. Two types of C1 domain were found, and the one lacking a short α-helix showed lower proportion. This finding suggests that short α-helices might be important to the stability of IgNAR. High-throughput sequencing revealed that the percentage of V_NAR types significantly vary between the diverse species of sharks. The variable region of IgNAR (the V_NAR) with small size and stabilization is a potential candidate for immunotherapeutic agents. The structure and stability analysis in this manuscript may be useful in future biomedical applications.

Deiminated proteins in extracellular vesicles and plasma of nurse shark (Ginglymostoma cirratum) - Novel insights into shark immunity

Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Extracellular vesicles are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins and extracellular vesicles (EVs) are described for the first time in shark plasma. We report a poly-dispersed population of shark plasma EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In plasma, 6 deiminated proteins, including complement and immunoglobulin, were identified, whereof 3 proteins were found to be exported in plasma-derived EVs. A PAD homologue was identified in shark plasma by Western blotting and detected an expected 70 kDa size. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in nurse shark plasma. This is the first report of deiminated proteins in plasma and EVs, highlighting a hitherto unrecognized post-translational modification in key immune proteins of innate and adaptive immunity in shark.

Shark IgNAR-derived binding domains as potential diagnostic and therapeutic agents

Many of the most successful drugs generated in recent years are based upon monoclonal antibodies (mAbs). However, for some therapeutic and diagnostic applications mAbs are far from ideal; for example, while their relatively large size and inherent receptor binding aids their longevity in vivo it can also limit their tissue penetration. Further, their structural complexity makes them expensive to produce and prone to denaturation in non-physiological environments. Thus, researchers have been searching for alternative antigen-binding molecules that can be utilized in situations where mAbs are suboptimal tools. One potential source currently being explored are the shark-derived binding domains known as VNARs. Despite their small size VNARs can bind antigens with high specificity and high affinity. Combined with their propensity to bind epitopes that are inaccessible to conventional mAbs, and their ability to resist denaturation, VNARs are an emerging prospect for use in therapeutic, diagnostic, and biotechnological applications.

Transcriptomic analysis of immunoglobulin novel antigen receptor (IgNAR) heavy chain constant domains of brownbanded bamboo shark (Chiloscyllium punctatum)

Cartilaginous fish are the evolutionarily oldest group of animals which possess antibodies, T cell receptors and major histocompatibility complex (MHC). The immunoglobulin novel antigen receptor (IgNAR) found in cartilaginous fish is a heavy chain homodimer which lacks light chain. The presence of non-canonical cysteine molecules and lack of CDR2 region make it more significant. To synthesize active binding domains based on variable region of IgNAR (VNAR), knowledge on the constant region dynamics play a significant role. The IgNAR exhibit species variations in its primary sequence features; hence, this study was conducted to determine the IgNAR heavy chain constant domain of the brownbanded bamboo shark (Chiloscyllium punctatum). Peripheral blood leukocytes (PBL) isolated from adult bamboo sharks were used to synthesize a cDNA library. A total of four billion residues of two million sequences (average length 218.41 bp) were obtained. Assembled sequences were aligned with published cartilaginous fish IgNAR constant region sequences. Transcriptome analysis revealed two distinct types of IgNAR in the brownbanded bamboo shark. Also, constant-1 domain sequences displayed 13 unique sequences which may reflect the least number of IgNAR gene clusters. The phylogenetic analysis revealed the closest relationship with the nurse shark (Ginglymostoma cirratum) followed by the wobbegong shark (Orectolobus maculatus) which belong to the same order Orectolobiformes. Analysis of the constant domains of the brownbanded bamboo shark IgNAR revealed an evolutionarily conserved nature and this knowledge can be used to design primers for VNAR cloning. Furthermore, knowledge on the structural features in IgNAR constant domains that increase the stability could be useful in the process of stabilizing human immunoglobulins.

Fish Immunoglobulins

The B cell receptor and secreted antibody are at the nexus of humoral adaptive immunity. In this review, we summarize what is known of the immunoglobulin genes of jawed cartilaginous and bony fishes. We focus on what has been learned from genomic or cDNA sequence data, but where appropriate draw upon protein, immunization, affinity and structural studies. Work from major aquatic model organisms and less studied comparative species are both included to define what is the rule for an immunoglobulin isotype or taxonomic group and what exemplifies an exception.

Antibody Repertoires in Fish

As in mammals, cartilaginous and teleost fishes possess adaptive immune systems based on antigen recognition by immunoglobulins (Ig), T cell receptors (TCR), and major histocompatibility complex molecules (MHC) I and MHC II molecules. Also it is well established that fish B cells and mammalian B cells share many similarities, including Ig gene rearrangements, and production of membrane Ig and secreted Ig forms. This chapter provides an overview of the IgH and IgL chains in cartilaginous and bony fish, including their gene organizations, expression, diversity of their isotypes, and development of the primary repertoire. Furthermore, when possible, we have included summaries of key studies on immune mechanisms such as allelic exclusion, somatic hypermutation, affinity maturation, class switching, and mucosal immune responses.

Construction of an artificially randomized IgNAR phage display library: screening of variable regions that bind to hen egg white lysozyme

To develop a multi-antigen-specific immunoglobulin new antigen receptor (IgNAR) variable (V) region phage display library, CDR3 in the V region of IgNAR from banded houndshark (Triakis scyllium) was artificially randomized, and clones specific for hen egg white lysozyme (HEL) were obtained by the biopanning method. The nucleotide sequence of CDR3 in the V region was randomly rearranged by PCR. Randomized CDR3-containing segments of the V region were ligated into T7 phage vector to construct a phage display library and resulted in a phage titer of 3.7 × 10(7) PFU/ml. Forty clones that contained randomized CDR3 inserts were sequenced and shown to have different nucleotide sequences. The HEL-specific clones were screened by biopanning using HEL-coated ELISA plates. After six rounds of screening, nine clones were identified as HEL-specific, eight of which showed a strong affinity to HEL in ELISA compared to a negative control (i.e., empty phage clone). The deduced amino acid sequences of CDR3 from the HEL-specific phage clones fell into four types (I-IV): type I contains a single cysteine residue and type II-IV contain two cysteine residues. These results indicated that the artificially randomized IgNAR library is useful for the rapid isolation of antigen-specific IgNAR V region without immunization of target antigen and showed that it is possible to isolate an antigen-specific IgNAR V region from this library.

Variable domain antibodies specific for viral hemorrhagic septicemia virus (VHSV) selected from a randomized IgNAR phage display library

Phage display libraries are used to screen for nucleotide sequences that encode immunoglobulin variable (V) regions that are specific for a target antigen. We previously constructed an immunoglobulin new antigen receptor (IgNAR) phage display library. Here we used this library to obtain an IgNAR V region that is specific for viral hemorrhagic septicemia virus (VHSV). A phage clone (clone 653) was found to be specific for VHSV by the biopanning method. The V region of clone 653 was used to construct a 6 × His tagged recombinant IgNAR-653 V protein (rIgNAR-653) using the Escherichia coli pET system. The rIgNAR-653 protein bound specifically to VHSV, confirming its activity.

Insights into the function of IgD

IgD, previously thought to be a recent addition to the immunoglobulin classes, has long been considered an enigmatic molecule. For example, it was debated if IgD had a specific function other than as an antigen receptor co-expressed with IgM on naive B cells and if it had an important role in mammalian immunity. However, during the past decade extensive sequencing of vertebrate genomes has shown that IgD homologs are present in all vertebrate taxa, except for birds. Moreover, recent functional studies indicate that IgD likely performs a unique role in vertebrate immune responses. The goal of this review is to summarize the IgD gene organization and structural data, which demonstrate that IgD has an ancient origin, and discuss the findings in catfish and humans that provide insight into the possible function of this elusive immunoglobulin isotype.

The immunoglobulin δ gene in jawed vertebrates: a comparative overview

Immunoglobulin D (IgD) was recently suggested to be an ancient Ig class, as old as IgM, arising approximately 500 million years ago. Its encoding gene has now been identified in nearly all classes of jawed vertebrates (except birds). Variance in the number of CH encoding exons and alternative RNA splicing confers this Ig class a marked structural plasticity, which differs substantially from IgM. Expression of the δ gene can be achieved through co-transcription with the μ gene or by class switching. Although a recent study has suggested that IgD functions as an immunomodulator in immunity and inflammation in humans, its functions are still far from clear. Further studies at the protein levels in additional species may help answer this question.