Crystal Structure of the Lamprey Variable Lymphocyte Receptor C Reveals an Unusual Feature in Its N-Terminal Capping Module

Jawless vertebrates represented by lampreys and hagfish use variable lymphocyte receptors (VLRs) as antigen receptors to mount adaptive immune responses. VLRs generate diversity that is comparable to immunoglobulins and T-cell receptors by a gene conversion-like mechanism, which is mediated by cytosine deaminases. Currently, three types of VLRs, VLRA, VLRB, and VLRC, have been identified in lampreys. Crystal structures of VLRA and VLRB in complex with antigens have been reported recently, but no structural information is available for VLRC. Here, we present the first crystal structure of VLRC from the Japanese lamprey (Lethenteron japonicum). Similar to VLRA and VLRB, VLRC forms a typical horseshoe-like solenoid structure with a variable concave surface. Strikingly, its N-terminal cap has a long loop with limited sequence variability that protrudes toward the concave surface, which is the putative antigen-binding surface. Furthermore, as predicted previously, its C-terminal cap lacks a highly variable protruding loop that plays an important role in antigen recognition by lamprey VLRA and VLRB. Recent work suggests that VLRC+ lymphocytes in jawless vertebrates might be akin to γδ T cells in jawed vertebrates. Structural features of lamprey VLRC described here suggest that it may recognize antigens in a unique manner.     

日本七鳃鳗(Lampetra japonica)VLRB的克隆表达及单克隆抗体制备

七鳃鳗(Lampetra japonica)和盲鳗(Hyperotreti)作为现存的无颌类脊椎动物的代表,其适应性免疫系统中的受体分子与哺乳动物的抗原受体分子不同,这种独特的受体分子称为可变淋巴细胞受体VLRs(Variable lym-phocyte receptors)。目前VLRs分为3类,分别是VLRA、VLRB、VLRC,而VLRB由七鳃鳗类B淋巴细胞产生,是其体液免疫中主要成分,与IgM结构和功能类似。文章对日本七鳃鳗VLRB基因保守的C末端进行克隆、原核表达和重组蛋白纯化后,免疫Balb/c小鼠,通过细胞融合及间接酶联免疫吸附实验(Enzyme-linked immu-nosorbent assay,ELISA)筛选技术得到针对VLRB保守区的单克隆抗体细胞株。将杂交瘤细胞接种小鼠腹腔得到大量的单抗腹水,经Protein G亲和纯化后的单抗进行ELISA与Western blotting检测。经ELISA检测抗体效价为1:40000。Western blotting结果显示该单克隆抗体能够特异的检测重组VLRB蛋白及七鳃鳗血清中分泌型VLRB。流式细胞实验证明该单抗能特异识别七鳃鳗类淋巴细胞表面表达的膜型VLRB。VLRB单克隆抗体的成功制备和建株,为研究日本七鳃鳗基于VLR的适应性免疫系统提供了重要的工具。     

Cloning and expression of VLRB of Lampetra japonica and generation of the corresponding monoclonal antibodies

The agnathans (lampreys and hagfishes) are representatives of the jawless vertebrates. The receptor molecules of adaptive immune system in lampreys are different from the antigen receptors in mammal vertebrates. The unique receptor molecules of lampreys are known as variable lymphocyte receptors (VLR). There are three types of VLRs in lampreys, VLRA, VLRB, and VLRC. Multimeric antigen-specific VLRB antibodies are secreted by VLRB+ lymphocytes and constitute the major components of the humoral arm of the lamprey adaptive immune system. Oligomeric VLRB antibodies are composed of four or five disulfide-linked dimeric subunits, which are similar to IgM antibodies in structure and function. In this study, the conservative c-terminal of Lampetra japonica VLRB was cloned and expressed in BL21 E. coli. The recombinant VLRB protein was purified by Ni2+ affinity chromatography column. After Balb/c mice immunity, cell fusion, the positive clones were screened by indirect enzyme-linked immunosorbent assay (ELISA). Finally, the hybridoma cells that produced specific anti-VLRB monoclonal antibodies were obtained. In order to get a large number of antibodies against VLRB, the hybridoma cells were injected into the abdominal cavity of Balb/c mice and the antibodies were purified by protein G sepharose. The results of ELISA indicated that the valence of anti-VLRB antibodies was 1:40000. Western blotting assay showed that the antibodies were able to detect both recombinant VLRB and secreted VLRB in lamprey sera. Flow cytometry analysis also revealed the existence of VLRB on the surface of lymphocytes. In summary, the anti-VLRB monoclonal antibodies provided a major tool for studying lamprey adaptive immune system.     

七鳃鳗鳃黏膜免疫系统类淋巴细胞免疫应答遗传基础

近年来,在无颌类脊椎动物七鳃鳗体内发现了以可变淋巴细胞受体(Variable lymphocyte receptors, VLR)为基础的抗原识别机制。为揭示七鳃鳗鳃黏膜免疫系统中类淋巴细胞适应性免疫应答的遗传基础,探索无颌类与有颌类脊椎动物在适应性免疫应答机制上的进化关系,本文构建了日本七鳃鳗(Lampetra japonica)鳃囊组织免疫前后cDNA文库并进行了高通量转录组测序及分析。通过对组装得到的88 525个独立基因(Unigene)进行功能注释,分别有21 704和9769个unigene在GO(Gene Ontology)和KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库得到注释。999个unigene参与免疫系统的多个通路,其中184个与高等脊椎动物TCR(T cell receptor)和BCR(B cell receptor)信号通路的51个分子具有较高的同源关系,说明七鳃鳗体内存在高等脊椎动物适应性免疫应答信号通路的相关分子。本文还发现5个VLRA、7个VLRB和4个VLRC分子,说明七鳃鳗鳃黏膜免疫组织内至少分布3种类淋巴细胞亚群。实时荧光定量PCR结果显示,Lck、Fyn和Zap70基因在免疫激发后表达量显著上调,而Syk、Btk和Blnk基因表达没有显著变化,说明七鳃鳗鳃组织受到抗原刺激后,类似T淋巴细胞的信号转导途径被激活。本研究初步证明,尽管无颌类和有颌类脊椎动物的适应性免疫系统在抗原识别机制上存在不同,但具有共同的遗传基础。研究结果为探讨七鳃鳗VLRA⁺、VLRB⁺和VLRC⁺淋巴细胞免疫应答信号传导过程提供了有价值的线索。     

Immune Related Genes Underpin the Evolution of Adaptive Immunity in Jawless Vertebrates

The study of immune related genes in lampreys and hagfish provides a unique perspective on the evolutionary genetic underpinnings of adaptive immunity and the evolution of vertebrate genomes. Separated from their jawed cousins at the stem of the vertebrate lineage, these jawless vertebrates have many of the gene families and gene regulatory networks associated with the defining morphological and physiological features of vertebrates. These include genes vital for innate immunity, inflammation, wound healing, protein degradation, and the development, signaling and trafficking of lymphocytes. Jawless vertebrates recognize antigen by using leucine-rich repeat (LRR) based variable lymphocyte receptors (VLRs), which are very different from the immunoglobulin (Ig) based T cell receptor (TCR) and B cell receptor (BCR) used for antigen recognition by jawed vertebrates. The somatically constructed VLR genes are expressed in monoallelic fashion by T-like and B-like lymphocytes. Jawless and jawed vertebrates thus share many of the genes that provide the molecular infrastructure and physiological context for adaptive immune responses, yet use entirely different genes and mechanisms of combinatorial assembly to generate diverse repertoires of antigen recognition receptors.     

The evolution of adaptive immune systems

A clonally diverse anticipatory repertoire in which each lymphocyte bears a unique antigen receptor is the central feature of the adaptive immune system that evolved in our vertebrate ancestors. The survival advantage gained through adding this type of adaptive immune system to a pre-existing innate immune system led to the evolution of alternative ways for lymphocytes to generate diverse antigen receptors for use in recognizing and repelling pathogen invaders. All jawed vertebrates assemble their antigen-receptor genes through recombinatorial rearrangement of different immunoglobulin or T cell receptor gene segments. The surviving jawless vertebrates, lampreys and hagfish, instead solved the receptor diversification problem by the recombinatorial assembly of leucine-rich-repeat genetic modules to encode variable lymphocyte receptors. The convergent evolution of these remarkably different adaptive immune systems involved innovative genetic modification of innate-immune-system components.     

Recognition of the Thomsen-Friedenreich Pancarcinoma Carbohydrate Antigen by a Lamprey Variable Lymphocyte Receptor

Variable lymphocyte receptors (VLRs) are leucine-rich repeat proteins that mediate adaptive immunity in jawless vertebrates. VLRs were recently shown to recognize glycans, such as the tumor-associated Thomsen-Friedenreich antigen (TFα; Galβ1–3GalNAcα), with a selectivity rivaling or exceeding that of lectins and antibodies. To understand the basis for TFα recognition by one such VLR (VLRB.aGPA.23), we measured thermodynamic parameters for the binding interaction and determined the structure of the VLRB.aGPA.23-TFα complex to 2.2 Å resolution. In the structure, four tryptophan residues form a tight hydrophobic cage encasing the TFα disaccharide that completely excludes buried water molecules. This cage together with hydrogen bonding of sugar hydroxyls to polar side chains explains the exquisite selectivity of VLRB.aGPA.23. The topology of the glycan-binding site of VLRB.aGPA.23 differs markedly from those of lectins or antibodies, which typically consist of long, convex grooves for accommodating the oligosaccharide. Instead, the TFα disaccharide is sandwiched between a variable loop and the concave surface of the VLR formed by the β-strands of the leucine-rich repeat modules. Longer oligosaccharides are predicted to extend perpendicularly across the β-strands, requiring them to bend to match the concavity of the VLR solenoid.     

VLR Recognition of TLR5 Expands the Molecular Characterization of Protein Antigen Binding by Non-Ig-based Antibodies

Variable lymphocyte receptors (VLRs) are unconventional adaptive immune receptors relatively recently discovered in the phylogenetically ancient jawless vertebrates, lamprey and hagfish. VLRs bind antigens using a leucine-rich repeat fold and are the only known adaptive immune receptors that do not utilize an immunoglobulin fold for antigen recognition. While immunoglobulin antibodies have been studied extensively, there are comparatively few studies on antigen recognition by VLRs, particularly for protein antigens. Here we report isolation, functional and structural characterization of three VLRs that bind the protein toll-like receptor 5 (TLR5) from zebrafish. Two of the VLRs block binding of TLR5 to its cognate ligand flagellin in functional assays using reporter cells. Co-crystal structures revealed that these VLRs bind to two different epitopes on TLR5, both of which include regions involved in flagellin binding. Our work here demonstrates that the lamprey adaptive immune system can be used to generate high-affinity VLR clones that recognize different epitopes and differentially impact natural ligand binding to a protein antigen.     

无颌类脊椎动物适应性免疫系统的研究进展

在以七鳃鳗和盲鳗为代表的无颌类脊椎动物中, 虽然发现了与有颌类脊椎动物T细胞受体(T-cell receptors, TLRs)、B细胞受体 (B-cell receptors, BCRs)可变区具有相似结构的先天性免疫受体, 却从未发现有颌类脊椎动物适应性免疫系统的核心组分: TCRs、BCRs、组织相容性复合体 (Major histocompatibility complex, MHC)。因此, 长期以来, 人们一直认为适应性免疫系统只存在于有颌类脊椎动物中。但最近的一项发现彻底改变了这一传统观念, 即在无颌类脊椎动物中, 存在一种新型可变淋巴细胞受体VLRs(Variable lymphocyte receptors), VLRs通过改变亮氨酸富集序列LRRs(Leucine-rich repeats)的插入情况, 实现对特异性抗原的高效识别。晶体衍射分析发现, 盲鳗的VLRs呈现一种“马蹄”型结构, 抗原结合位点则位于“马蹄”的凹面区。分泌型的VLRs以四聚体或五聚体的形式识别、结合特异性抗原。综上所述, 无颌类和有颌类脊椎动物应用不同的抗原识别系统完成适应性免疫反应。文章对近年来无颌类脊椎动物适应性免疫系统相关分子的研究进展加以概述, 为揭示适应性免疫系统起源与进化问题提供有益参考。     

Variable domains in hagfish: NICIR is a polymorphic multigene family expressed preferentially in leukocytes and is related to lamprey TCR-like

The jawless vertebrates, represented by hagfish and lampreys, are the most advanced animals that apparently lack T cell and B cell receptors. As such, they offer unique opportunities for understanding the evolution of antigen receptors and variable (V)-type immunoglobulin (Ig)-like domains. In the present study, we describe four hagfish Ig superfamily (IgSF) members carrying V-type domains. None of them appeared to have direct counterparts in jawed vertebrates, indicating that many IgSF molecules have either evolved independently in jawed and jawless vertebrates or diverged to the extent that clear homology is no longer recognizable. One of the members encoded a molecule closely related to the previously described membrane protein designated novel ITAM (immunoreceptor tyrosine-based activation motif)-containing IgSF receptors (NICIR). We show here that NICIR is a polymorphic multigene family with at least three members and is expressed predominantly in peripheral blood leukocytes. Phylogenetic analysis indicates that among known proteins, NICIR is most closely related to the lamprey molecule recently proposed to be a potential ancestor of T cell receptors.Sequence data reported in this paper were submitted to the DDBJ/EMBL/GenBank databases under accession nos. AB234206-AB234210, AB242215-AB224219, and AB242221-AB242223.     

Structural diversity of the hagfish variable lymphocyte receptors

Variable lymphocyte receptors (VLRs) are recently discovered leucine-rich repeat (LRR) family proteins that mediate adaptive immune responses in jawless fish. Phylogenetically it is the oldest adaptive immune receptor and the first one with a non-immunoglobulin fold. We present the crystal structures of one VLR-A and two VLR-B clones from the inshore hagfish. The hagfish VLRs have the characteristic horseshoe-shaped structure of LRR family proteins. The backbone structures of their LRR modules are highly homologous, and the sequence variation is concentrated on the concave surface of the protein. The conservation of key residues suggests that our structures are likely to represent the LRR structures of the entire repertoire of jawless fish VLRs. The analysis of sequence variability, prediction of protein interaction surfaces, amino acid composition analysis, and structural comparison with other LRR proteins suggest that the hypervariable concave surface is the most probable antigen binding site of the VLR.     

Regulation of antigen‐receptor gene assembly in hagfish

Variable lymphocyte receptors (VLRs) are antigen receptors in the jawless vertebrates lamprey and hagfish. VLR genes are classified into VLRA and VLRB, and lymphocytes expressing VLRA are T‐cell‐like, whereas those expressing VLRB are B‐cell‐like in the sea lamprey. Diverse VLR genes are assembled somatically in lymphocytes; however, how the assembly is regulated is still largely unknown. Here, we analyse VLR gene assembly at the single‐cell level in the inshore hagfish (Eptatretus burgeri). Each lymphocyte assembles and transcribes only one type of VLR gene, either VLRA or VLRB. In general, monoallelic assembly of VLR was observed, but diallelic assembly was found in some cases—in many of which, one allele was functional and the other was defective. In fact, all VLR‐assembled lymphocytes contained at least one functional VLR gene. Together, these results indicate a feedback inhibition of VLR assembly and selection of VLR‐positive lymphocytes.     

临床诊断与治疗的新工具——可变淋巴细胞受体

单克隆抗体(Monoclonal antibody, mAb)在癌症以及自身免疫等疾病的诊断与治疗中得到广泛应用, 并且取得了重大进展。当今应用于临床的单克隆抗体是在免疫球蛋白的基础上进行改造研发而得。然而近期发现的无颌类脊椎动物的特异性抗原受体-可变淋巴细胞受体(Variable lymphocyte receptor, VLR), 为抗体类试剂或药物的研发提供了新的视角。与免疫球蛋白(Immunoglobulins, Ig)相比, VLR与抗原结合的特异性、亲和力及稳定性都优于Ig类抗体, 并且抗原特异性单克隆VLR的制备技术日趋成熟。因此, VLR在临床诊断和治疗中具有更高的应用价值, 并可能成为新一代的抗体药物。文章就VLR的基本特征、制备方法及其应用前景进行综述, 为实现VLR在临床诊断与治疗等领域中的应用提供有益参考。     

A human memory T cell subset with stem cell-like properties

Immunological memory is thought to depend on a stem cell-like, self-renewing population of lymphocytes capable of differentiating into effector cells in response to antigen re-exposure. Here we describe a long-lived human memory T cell population that has an enhanced capacity for self-renewal and a multipotent ability to derive central memory, effector memory and effector T cells. These cells, specific to multiple viral and self-tumor antigens, were found within a CD45RO(-), CCR7(+), CD45RA(+), CD62L(+), CD27(+), CD28(+) and IL-7Rα(+) T cell compartment characteristic of naive T cells. However, they expressed large amounts of CD95, IL-2Rβ, CXCR3, and LFA-1, and showed numerous functional attributes distinctive of memory cells. Compared with known memory populations, these lymphocytes had increased proliferative capacity and more efficiently reconstituted immunodeficient hosts, and they mediated superior antitumor responses in a humanized mouse model. The identification of a human stem cell-like memory T cell population is of direct relevance to the design of vaccines and T cell therapies.     

IL-4-induced lymphokine-activated killer cells. Lytic activity is mediated by phenotypically distinct natural killer-like and T cell-like large granular lymphocytes

The purpose of the current study was to characterize lymphokine-activated killer (LAK) activity induced with IL-4/B cell stimulatory factor-1 and to compare IL-4-induced LAK activity with IL-2-induced LAK activity. Culture of murine lymphocytes with high concentrations of IL-4 induced nonspecific lytic activity against a wide variety of tumors. Lytic activity induced by IL-4 increased with increasing concentrations of IL-4 over the range of 1.0 to 25 ng/ml. The kinetics of LAK induction by IL-4 and IL-2 were similar; however, IL-4 was less effective than IL-2 in maintaining lytic activity for longer culture periods and provided lower viable cell yields than did IL-2. Similar to IL-2, IL-4 induced blastogenesis and the generation of large granular lymphocytes, all LAK activity observed was exclusively associated with the large granular lymphocyte fraction, and the cytolytic effector cells were heterogeneous in regards to cell surface phenotype. The majority of IL-4-induced lytic activity was associated with mutually exclusive NK-like (i.e., NK-1.1+ Lyt-2-) and T cell-like (i.e., NK-1.1- Lyt-2+) LAK cells. The precursors for each subset were distinct and expressed the asialo-GM1+ Lyt-2- and the asialo-GM1+ Lyt-2+ phenotypes, respectively. Although IL-4-induced LAK effector cells were morphologically and phenotypically similar to IL-2-induced LAK cells, IL-2 generated equivalent numbers of T cell-like and NK-like LAK cells, whereas IL-4 generated 3.5-fold more T cell-like LAK cells than NK-like LAK cells. It might eventually be possible to exploit the preferential activation of T cell-like LAK by IL-4 for therapeutic advantage.     

Cross-reactivity between human and canine helper and suppressor T cell antigens using monoclonal antibodies RPA-T4 and HuLy-m8

The murine monoclonal antibodies RPA-T4 and HuLy-m8, specific for a framework determinant of human helper/inducer and suppressor/cytotoxic T cell antigens, cross-reacted with canine cell membrane molecules recognizing a biomolecular complex (50,000 to 55,000 daltons) similar to that described in humans. We investigated the distribution of these helper and suppressor T cell-like antigens on canine peripheral blood lymphocytes. With complement-mediated lymphocytotoxicity, 34% and 35% of the canine lymphocytes expressed the helper T cell-like antigens and the suppressor-like T cell antigens, respectively. When the lymphocytes were treated with RPA-T4 and HuLy-m8, the respective helper and suppressor function was significantly inhibited.     

Design principles of adaptive immune systems

Both jawless vertebrates, such as lampreys and hagfish, and jawed vertebrates (encompassing species as diverse as sharks and humans) have an adaptive immune system that is based on somatically diversified and clonally expressed antigen receptors. Although the molecular nature of the antigen receptors and the mechanisms of their assembly are different, recent findings suggest that the general design principles underlying the two adaptive immune systems are surprisingly similar. The identification of such commonalities promises to further our understanding of the mammalian immune system and to inspire the development of new strategies for medical interventions targeting the consequences of faulty immune functions.