The antibody repertoire in evolution: chance, selection, and continuity

Large-scale data mining of four billion human antibody variable regions reveals convergence between therapeutic and natural antibodies that constrains search space for biologics drug discovery

The naïve human antibody repertoire has theoretical access to an estimated > 1015 antibodies. Identifying subsets of this prohibitively large space where therapeutically relevant antibodies may be found is useful for development of these agents. It was previously demonstrated that, despite the immense sequence space, different individuals can produce the same antibodies. It was also shown that therapeutic antibodies, which typically follow seemingly unnatural development processes, can arise independently naturally. To check for biases in how the sequence space is explored, we data mined public repositories to identify 220 bioprojects with a combined seven billion reads. Of these, we created a subset of human bioprojects that we make available as the AbNGS database (https://naturalantibody.com/ngs/). AbNGS contains 135 bioprojects with four billion productive human heavy variable region sequences and 385 million unique complementarity-determining region (CDR)-H3s. We find that 270,000 (0.07% of 385 million) unique CDR-H3s are highly public in that they occur in at least five of 135 bioprojects. Of 700 unique therapeutic CDR-H3, a total of 6% has direct matches in the small set of 270,000. This observation extends to a match between CDR-H3 and V-gene call as well. Thus, the subspace of shared ('public') CDR-H3s shows utility for serving as a starting point for therapeutic antibody design.

Understanding the human antibody repertoire

The origins of the various elements in the human antibody repertoire have been and still are subject to considerable uncertainty. Uncertainty in respect of whether the various elements have always served a specific defense function or whether they were co-opted from other organismal roles to form a crude naïve repertoire that then became more complex as combinatorial mechanisms were added. Estimates of the current size of the human antibody naïve repertoire are also widely debated with numbers anywhere from 10 million members, based on experimentally derived numbers, to in excess of one thousand trillion members or more, based on the different sequences derived from theoretical combinatorial calculations. There are questions that are relevant at both ends of this number spectrum. At the lower bound it could be questioned whether this is an insufficient repertoire size to counter all the potential antigen-bearing pathogens. At the upper bound the question is rather simpler: How can any individual interrogate such an astronomical number of antibody-bearing B cells in a timeframe that is meaningful? This review evaluates the evolutionary aspects of the adaptive immune system, the calculations that lead to the large repertoire estimates, some of the experimental evidence pointing to a more restricted repertoire whose variation appears to derive from convergent 'structure and specificity features', and includes a theoretical model that seems to support it. Finally, a solution that may reconcile the size difference anomaly, which is still a hot subject of debate, is suggested.

Acquired protective immune response in a fish-myxozoan model encompasses specific antibodies and inflammation resolution

The myxozoan parasite Enteromyxum leei causes chronic enteritis in gilthead sea bream (GSB, Sparus aurata) leading to intestinal dysfunction. Two trials were performed in which GSB that had survived a previous infection with E. leei (SUR), and naïve GSB (NAI), were exposed to water effluent containing parasite stages. Humoral factors (total IgM and IgT, specific anti-E. leei IgM, total serum peroxidases), histopathology and gene expression were analysed. Results showed that SUR maintained high levels of specific anti-E. leei IgM (up to 16 months), expressed high levels of immunoglobulins at the intestinal mucosa, particularly the soluble forms, and were resistant to re-infection. Their acquired-type response was complemented by other immune effectors locally and systemically, like cell cytotoxicity (high granzyme A expression), complement activity (high c3 and fucolectin expression), and serum peroxidases. In contrast to NAI, SUR displayed a post-inflammatory phenotype in the intestine and head kidney, characteristic of inflammation resolution (low il1β, high il10 and low hsp90α expression).

Establishing Correlates of Protection for Vaccine Development: Considerations for the Respiratory Syncytial Virus Vaccine Field

Correlates of protection (CoPs) can play a significant role in vaccine development by assisting the selection of vaccine candidates for clinical trials, supporting clinical trial design and implementation, and simplifying tests of vaccine modifications. Because of this important role in vaccine development, it is essential that CoPs be defined by well-designed immunogenicity and efficacy studies, with attention paid to benefits and limitations. The respiratory syncytial virus (RSV) field is unique in that a great deal of information about the humoral response is available from basic research and clinical studies. Polyclonal and monoclonal antibodies have been used routinely in the clinic to protect vulnerable infants from infection, providing a wealth of information about correlations between neutralizing antibodies and disease prevention. Considerations for the establishment of future CoPs to support RSV vaccine development in different populations are therefore discussed.

Linking autoimmunity to the origin of the adaptive immune system

In jawed vertebrates, the adaptive immune system (AIS) cooperates with the innate immune system (IIS) to protect hosts from infections. Although targeting non-self-components, the AIS also generates self-reactive antibodies which, when inadequately counter-selected, can give rise to autoimmune diseases (ADs). ADs are on the rise in western countries. Why haven’t ADs been eliminated during the evolution of a ∼500 million-year old system? And why have they become more frequent in recent decades? Self-recognition is an attribute of the phylogenetically more ancient IIS and empirical data compellingly show that some self-reactive antibodies, which are classifiable as elements of the IIS rather then the AIS, may protect from (rather than cause) ADs. Here, we propose that the IIS’s self-recognition system originally fathered the AIS and, as a consequence of this relationship, its activity is dampened in hygienic environments. Rather than a mere breakdown or failure of the mechanisms of self-tolerance, ADs might thus arise from architectural constraints.

Immune system and immune responses in fish and their role in comparative immunity study: a model for higher organisms

The basal position of fish in vertebrate phylogeny makes them very attractive for genomic and functional comparative immunity studies. Adaptive immunity arose early in vertebrate evolution, 450 million years ago between the divergence of cyclostomes and cartilaginous fish. The fundamental immune molecules, which include Ag-recognizing lymphocytes, immunoglobulins (Abs and Ig-family TCR), MHC products, and recombination-activating (RAG) 1 and 2 genes and the recombination mechanisms (cause of diversity in TCRs and Igs) are similar in fish and mammals. These molecules and their immune response mechanisms unravelled the primordial vertebrate immune system repertoire and adaptive radiations. Moreover, screening of animal models like zebrafish has a great importance to discover genes involved in T cell development, thymic organogenesis, and in immunity to infections. The zebrafish model may also be useful for cancer research due to its various features like rapid development, tractable genetics, ease in in vivo imaging and chemical screening.

Naturally occurring autoantibodies in mediating clearance of senescent red blood cells

Germline-encoded naturally occurring autoantibodies (NAbs) developed about 400 to 450 million years ago to provide specificity for clearance ofbody waste in animals with 3 germ layers. Such NAbs became a necessity to selectively clear aged red blood cells (RBC) surviving 60 to 120 d in higher vertebrates. IgG NAbs to senescent RBC are directed to the most abundant integral membrane protein, the anion-transport protein or band 3 protein, but only bind firmly upon its oligomerization, which facilitates bivalent binding. The main constituent of RBC, the oxygen-carrying hemoglobin, is susceptible to oxidative damage. Oxidized hemoglobin forms hemichromes (a form of aggregates) that bind to the cytoplasmic portion of band 3 protein, induces their clustering on the cytoplasmic, as well as the exoplasmic side and thereby provides the prerequisites for the low affinity IgG anti-band 3 NAbs to bind bivalently. Bound anti-band 3 NAbs overcome their low numbers per RBC by stimulating complement amplification. An affinity for C3 outside the antigen binding region is responsible for a preferential formation of C3b(2)-IgG complexes from anti-band 3 NAbs. These complexes first bind oligomeric properdin, which enhances their affinity for factor B in assembling an alternative C3 convertase.

Going adaptive: the saga of antibodies

Because of their extreme importance to human health, we probably know more about the structure and function of antibodies than practically any other molecule. Despite all the knowledge that has been accrued in the understanding of antibodies, modern approaches, especially comparative genomics, continue to yield novel findings regarding their underlying biology and evolution. In this review, we describe recent research that led to these revelations, and discuss the broad evolutionary implications of these findings. We have restricted our discussion to three vignettes. Considerable attention has been paid to the recent discovery that the teleost IgH locus is highly similar in organization to the Tcra-Tcrd locus, implicating an evolutionary common ancestor and parallels between the functions of B and T cells during development. Second, we discuss how a new type of antibody, recently discovered in jawless vertebrates, composed not of immunoglobulins but leucine-rich repeats, sheds new light on the overall forces driving evolution of all adaptive antigen receptors. Lastly, we discuss how accumulation of genomic sequences of various human subpopulations leads to better understanding of the directionality of antibody evolution. There is always more to learn from the unfolding saga of antibodies.

Immunoglobulins, antibody repertoire and B cell development

Swine share with most placental mammals the same five antibody isotypes and same two light chain types. Loci encoding lambda, kappa and Ig heavy chains appear to be organized as they are in other mammals. Swine differ from rodents and primates, but are similar to rabbits in using a single VH family (VH3) to encode their variable heavy chain domain, but not the family used by cattle, another artiodactyl. Distinct from other hoofed mammals and rodents, Ckappa:Clambda usage resembles the 1:1 ratio seen in primates. Since IgG subclasses diversified after speciation, same name subclass homologs do not exist among swine and other mammals unless very closely related. Swine possess six putative IgG subclasses that appear to have diversified by gene duplication and exon shuffle while retaining motifs that can bind to FcgammaRs, FcRn, C1q, protein A and protein G. The epithelial chorial placenta of swine and the precosial nature of their offspring have made piglets excellent models for studies on fetal antibody repertoire development and on the postnatal role of gut colonization, maternal colostrum and neonatal infection on the development of adaptive immunity during the "critical window" of immunological development. This chapter traces the study of the humoral immune system of this species through its various eras of discovery and compiles the results in tables and figures that should be a useful reference for educators and investigators.

Isolator and other neonatal piglet models in developmental immunology and identification of virulence factors

The postnatal period is a ‘critical window’, a time when innate and passive immunity protect the newborn mammal while its own adaptive immune system is developing. Neonatal piglets, especially those reared in isolators, provide valuable tools for studying immunological development during this period, since environmental factors that cause ambiguity in studies with conventional animals are controlled by the experimenter. However, these models have limited value unless the swine immune system is first characterized and the necessary immunological reagents developed. Characterization has revealed numerous features of the swine immune system that did not fit mouse paradigms but may be more generally true for most mammals. These include fetal class switch recombination that is uncoupled from somatic hypermutation, the relative importance of the molecular mechanisms used to develop the antibody repertoire, the role of gut lymphoid tissue in that process, and the limited heavy chain repertoire but diverse IgG subclass repertoire. Knowledge gained from studies of adaptive immunity in isolator-reared neonatal pigs suggests that isolator piglets can be valuable in identification of virulence factors that are often masked in studies using conventional animals.

Naturally occurring auto-antibodies in homeostasis and disease

Antibodies with germline or close to germline configuration exist in vertebrates, and these so-called 'naturally occurring auto-antibodies' (NAb) are directed to self and altered self components. Such NAbs have been attracting increasing interest because several of them, including some in their recombinant forms, have therapeutic potential. Whereas a large number of IgM and IgG NAbs have tissue homeostatic roles, others modulate and regulate cellular and enzyme properties. This review describes some of these NAbs and emphasizes how these low-titer, low-affinity NAbs interact with self and altered self and show functional potency in homeostasis and regulation, in addition to in diseases such as infarction and systemic inflammatory response syndrome.

The isolator piglet: a model for studying the development of adaptive immunity

The period from late gestation to weaning in neonatal mammals is a critical window when the adaptive immune system develops and replaces the protection temporarily provided by passive immunity and pre-adaptive antibodies. It is also when oral tolerance to dietary antigen and the distinction between commensal and pathogenic gut bacteria becomes established resulting in immune homeostasis. The reproductive biology of swine provides a unique model for distinguishing the effects of different factors on immune development during this critical period because all extrinsic factors are controlled by the experimenter. This chapter reviews this early stage of development and the usefulness of the piglet model for understanding events during this transitional stage. The review also describes the major features of the porcine immune system and the immune stimulatory and dysregulatory factors that act during this period. The value of the model to medical science in such areas as food allergy, organ transplantation, cystic fibrosis and the production of humanized antibodies for immuno-therapy is discussed.

Naturally occurring B-cell autoreactivity: A critical overview

In over one century of research in immunology marked progress in the scientific knowledge and the implications derived from it has been made. At the same time several contradictory and seemingly opposing results have been obtained. The term autoimmunity is still conceived by many as a term directly related to an immunopathological state. However, strong evidence exist that not only the immune system is able to recognize self-constituents, but it appears also that this property is essential for homeostasis. Direct or indirect alterations of such self-recognition properties of the immune system may contribute to pathology. In this review, the most recent advances in the field of naturally occurring B-cell autoreactivity in health as well as in disease are presented and discussed.

Homeostatic roles of naturally occurring antibodies: An overview

Immunoglobulins may have been developed in evolution to provide specificity for clearing body waste in the first animals with three germ layers. Tissue homeostasis in vertebrates comprises clearance of proteins released from lysed cells, elimination of altered plasma proteins, of senescent and apoptotic cells. Rather specific IgM and IgG naturally occurring antibodies (NAbs) to cytoplasmic and cytoskeletal proteins bind to proteins released from lysing cells and the IgG NAbs are slightly upregulated upon demand. Some of these NAbs along with complement have devastating effects when massive amounts of intracellular proteins are released during an infarct or an ischemia/reperfusion experiment. IgM NAbs to neoepitopes on plasma proteins/lipids help clear denatured proteins and are protective. IgG NAbs to an exposed protein, band 3 from red blood cells, bind to oligomerized band 3 and due to an affinity for C3 within their framework preferentially form C3b2-IgG complexes from nascent C3b. Thus, anti-band 3 NAbs gain potency by using avidity and generating a potent precursor of the amplifying C3 convertase. IgM NAbs to neoepitopes, which are generated by oxidized lipids forming Schiff bases with proteins, are protective and help clear this waste in atherosclerosis, but IgG antibodies (NAbs?) of the same specificity promote disease.

Antibody binding loop insertions as diversity elements

In the use of non-antibody proteins as affinity reagents, diversity has generally been derived from oligonucleotide-encoded random amino acids. Although specific binders of high-affinity have been selected from such libraries, random oligonucleotides often encode stop codons and amino acid combinations that affect protein folding. Recently it has been shown that specific antibody binding loops grafted into heterologous proteins can confer the specific antibody binding activity to the created chimeric protein. In this paper, we examine the use of such antibody binding loops as diversity elements. We first show that we are able to graft a lysozyme-binding antibody loop into green fluorescent protein (GFP), creating a fluorescent protein with lysozyme-binding activity. Subsequently we have developed a PCR method to harvest random binding loops from antibodies and insert them at predefined sites in any protein, using GFP as an example. The majority of such GFP chimeras remain fluorescent, indicating that binding loops do not disrupt folding. This method can be adapted to the creation of other nucleic acid libraries where diversity is flanked by regions of relative sequence conservation, and its availability sets the stage for the use of antibody loop libraries as diversity elements for selection experiments.

The evolution of immune mechanisms

From early on in evolution, organisms have had to protect themselves from pathogens. Mechanisms for discriminating "self" from "non-self" evolved to accomplish this task, launching a long history of host-pathogen co-evolution. Evolution of mechanisms of immune defense has resulted in a variety of strategies. Even unicellular organisms have rich arsenals of mechanisms for protection, such as restriction endonucleases, antimicrobial peptides, and RNA interference. In multicellular organisms, specialized immune cells have evolved, capable of recognition, phagocytosis, and killing of foreign cells as well as removing their own cells changed by damage, senescence, infection, or cancer. Additional humoral factors, such as the complement cascade, have developed that co-operate with cellular immunity in fighting infection and maintaining homeostasis. Defensive mechanisms based on germline-encoded receptors constitute a system known as innate immunity. In jaw vertebrates, this system is supplemented with a second system, adaptive immunity, which in contrast to innate immunity is based on diversification of immune receptors and on immunological memory in each individual.Usually, each newly evolved defense mechanism did not replace the previous one, but supplemented it, resulting in a layered structure of the immune system. The immune system is not one system but rather a sophisticated network of various defensive mechanisms operating on different levels, ranging from mechanisms common for every cell in the body to specialized immune cells and responses at the level of the whole organism. Adaptive changes in pathogens have shaped the evolution of the immune system at all levels.