If the immune repertoire evolved to be large, random, and somatically generated, then

Regulatory T cells and co-evolution of allele-specific MHC recognition by the TCR

What is the evolutionary mechanism for the TCR-MHC-conserved interaction? We extend Dembic's model (Dembic Z. In, Scand J Immunol e12806, 2019) of thymus positive selection for high-avidity anti-self-MHC Tregs among double (CD4 + CD8+)-positive (DP) developing thymocytes. This model is based on competition for self-MHC (+ Pep) complexes presented on cortical epithelium. Such T cells exit as CD4 + CD25+FoxP3 + thymic-derived Tregs (tTregs). The other positively selected DP T cells are then negatively selected on medulla epithelium removing high-avidity anti-self-MHC + Pep as T cells commit to CD4 + or CD8 + lineages. The process is likened to the competitive selection and affinity maturation in Germinal Centre for the somatic hypermutation (SHM) of rearranged immunoglobulin (Ig) variable region (V[D]Js) of centrocytes bearing antigen-specific B cell receptors (BCR). We now argue that the same direct SHM processes for TCRs occur in post-antigenic Germinal Centres, but now occurring in peripheral pTregs. This model provides a potential solution to a long-standing problem previously recognized by Cohn and others (Cohn M, Anderson CC, Dembic Z. In, Scand J Immunol e12790, 2019) of how co-evolution occurs of species-specific MHC alleles with the repertoire of their germline TCR V counterparts. We suggest this is not by 'blind', slow, and random Darwinian natural selection events, but a rapid structured somatic selection vertical transmission process. The pTregs bearing somatic TCR V mutant genes then, on arrival in reproductive tissues, can donate their TCR V sequences via soma-to-germline feedback as discussed in this journal earlier. (Steele EJ, Lindley RA. In, Scand J Immunol e12670, 2018) The high-avidity tTregs also participate in the same process to maintain a biased, high-avidity anti-self-MHC germline V repertoire.

Germline V repertoires: Origin, maintenance, diversification

In our view, Melvin Cohn (Scand J Immunol. 2018;87:e12640) has set out the logical guidelines towards a resolution of the very real enigma of the selectability of vertebrate germline Ig V repertoires under the current evolutionary paradigm…" A somatically derived repertoire scrambles this (germline VL + VH) substrate so that its specificities are lost, making it un-selectable in the germline. Consequently, evolution faced an incompatibility." It is argued here in Reply that a reverse transcriptase-based soma-to-germline process (S->G) targeting germline V segment arrays goes some considerable way to resolving fundamental contradictions on the origin, maintenance and then real-time adaptive diversification of these limited sets of V segments encoded within various V repertoire arrays.

Thoughts engendered by Bretscher's Two-step, Two-signal model for a peripheral self-non-self discrimination and the origin of primer effector T helpers

There are three questions under re-examination here that have been inspired by Bretscher's 'Two-step, Two-signal' model. First, what is the nature of the steps required in order for antigen-responsive cells to become effectors? Second, how does the immune system get started? Third and the most troublesome, what is the mechanism that relates the delivery of the two signals? To answer the first question, Bretscher proposes a pathway that I will place in another context by comparing it with what had been envisaged under the Associative Recognition of Antigen (ARA) model. The second question, how does the immune system gets started, is crucial to our understanding of the self-non-self discrimination. This problem boils down to, what is the origin of the first effector T helper (eTh) cells required to activate all antigen-responsive cells including the T helpers themselves (the primer problem)? To deal with this question, I proposed an antigen-independent pathway to primer eTh. Bretscher presents us with an antigen-dependent pathway to primer eTh. As competing models are precious in clarifying thinking and in guiding experimentation, I felt it important to reanalyse the two models and look for ways to decide between them. The third question deals with the requirement for and the mechanism of associative (linked) recognition of antigen (ARA). The concept of ARA is so compelling at both the experimental and theoretical levels that to save it, a new perspective will be introduced.

Violation of an evolutionarily conserved immunoglobulin diversity gene sequence preference promotes production of dsDNA-specific IgG antibodies

Variability in the developing antibody repertoire is focused on the third complementarity determining region of the H chain (CDR-H3), which lies at the center of the antigen binding site where it often plays a decisive role in antigen binding. The power of VDJ recombination and N nucleotide addition has led to the common conception that the sequence of CDR-H3 is unrestricted in its variability and random in its composition. Under this view, the immune response is solely controlled by somatic positive and negative clonal selection mechanisms that act on individual B cells to promote production of protective antibodies and prevent the production of self-reactive antibodies. This concept of a repertoire of random antigen binding sites is inconsistent with the observation that diversity (D_H) gene segment sequence content by reading frame (RF) is evolutionarily conserved, creating biases in the prevalence and distribution of individual amino acids in CDR-H3. For example, arginine, which is often found in the CDR-H3 of dsDNA binding autoantibodies, is under-represented in the commonly used D_H RFs rearranged by deletion, but is a frequent component of rarely used inverted RF1 (iRF1), which is rearranged by inversion. To determine the effect of altering this germline bias in D_H gene segment sequence on autoantibody production, we generated mice that by genetic manipulation are forced to utilize an iRF1 sequence encoding two arginines. Over a one year period we collected serial serum samples from these unimmunized, specific pathogen-free mice and found that more than one-fifth of them contained elevated levels of dsDNA-binding IgG, but not IgM; whereas mice with a wild type D_H sequence did not. Thus, germline bias against the use of arginine enriched D_H sequence helps to reduce the likelihood of producing self-reactive antibodies.

Sequencing of modern Lepus VDJ genes shows that the usage of VHn genes has been retained in both Oryctolagus and Lepus that diverged 12 million years ago

Among mammals, the European rabbit (Oryctolagus cuniculus) has a unique mechanism of generating the primary antibody repertoire. Despite having over 200 VH genes, the VH1 gene, the most D-proximal VH gene, is used in 80-90 % of VDJ rearrangements, while the remaining 10-20 % is encoded by the VHn genes that map at least 100 Kb upstream of VH1. The maintenance of the VHn genes usage in low frequency in VDJ rearrangements has been suggested to represent a relic of an ancestral immunologic response to pathogens. To address this question, we sequenced VDJ genes for another leporid, genus Lepus, which separated from European rabbit 12 million years ago. Approximately 25 VDJ gene sequences were obtained for each one of three Lepus europaeus individuals. We found that Lepus also uses the VHn genes in 5-10 % of its VDJ rearrangements. Our results show that the VHn genes are a conserved ancestral polymorphism that has been maintained in the leporids genome and is being used for the generation of VDJ rearrangements by both modern Lepus and Oryctolagus.

Epitope reactions can be gauged by relative antibody discriminating specificity (RADS) values supported by deletion, substitution and cysteine bridge formation analyses: potential uses in pathogenesis studies

Background

Epitope-mapping of infectious agents is essential for pathogenesis studies. Since polyclonal antibodies (PAbs) and monoclonal antibodies (MAbs) are always polyspecific and can react with multiple epitopes, it is important to distinguish between specific and non-specific reactions. Relative antibody discriminating specificity (RADS) values, obtained from their relative ELISA reactions with L-amino acid peptides prepared in the natural versus reverse orientations (x-fold absorbance natural/absorbance reverse = RADS value) may be valuable for this purpose.

PAbs generated against the dengue type-2 virus (DENV-2) nonstructural-1 (NS1) glycoprotein candidate vaccine also reacted with both DENV envelope (E) glycoproteins and blood-clotting proteins. New xKGSx/xSGKx amino acid motifs were identified on DENV-2 glycoproteins, HIV-1 gp41 and factor IXa. Their potential roles in DENV and HIV-1 antibody-enhanced replication (AER) and auto-immunity were assessed.

In this study, a) RADS values were determined for MAbs and PAbs, generated in congeneic (H2: class II) mice against DENV NS1 glycoprotein epitopes, to account for their cross-reaction patterns, and b) MAb 1G5.3 reactions with xKGSx/xSGKx motifs present in the DENV-4 NS1, E and HIV-1 glycoproteins and factor IXa were assessed after the introduction of amino acid substitutions, deletions, or intra-/inter-cysteine (C-C) bridges.

Results

MAbs 1H7.4, 5H4.3, 3D1.4 and 1G5.3 had high (4.23- to 16.83-fold) RADS values against single epitopes on the DENV-2 NS1 glycoprotein, and MAb 3D1.4 defined the DENV complex-conserved LX1 epitope. In contrast, MAbs 1G5.4-A1-C3 and 1C6.3 had low (0.47- to 1.67-fold) RADS values against multiple epitopes. PAb DENV complex-reactions occurred through moderately-high (2.77- and 3.11-fold) RADS values against the LX1 epitope. MAb 1G5.3 reacted with xSGKx motifs present in DENV-4 NS1 and E glycoproteins, HIV-1 gp41 and factor IXa, while natural C-C bridge formations or certain amino acid substitutions increased its binding activity.

Conclusions

These results: i) were readily obtained using a standard 96-well ELISA format, ii) showed the LX1 epitope to be the immuno-dominant DENV complex determinant in the NS1 glycoprotein, iii) supported an antigenic co-evolution of the DENV NS1 and E glycoproteins, and iv) identified methods that made it possible to determine the role of anti-DENV PAb reactions in viral pathogenesis.

On the opposing views of the self-nonself discrimination by the immune system

Today's generally accepted view of the self-nonself discrimination was voiced by Miller(1) in 2004 in a thought-provoking essay. In spite of its popularity, this position has its limitations, which are analyzed here with a view toward establishing an interactive discussion that hopefully will culminate in agreed upon decisive experiments. The inadequacies of Miller's view of the self-nonself discrimination and their resolution under the associative recognition of antigen model are analyzed.

Regulatory T cells and immune computation

The role of Treg in immune regulation is the topic of this Viewpoint series in the European Journal of Immunology (EJI); the question to be discussed in this section is the effector function of Treg in immune regulation. In this manuscript, we take on the following three postulates outlined by Rolf Zinkernagel on the role of Treg in the control of immunity. First, the immune response is regulated primarily by the antigen and not by Treg. Second, immune non-responsiveness results from the deletion of specific receptor-bearing T cells. Third, there is no definitive proof of the existence of specialized Treg that know what is needed for an equilibrated immune response. Herein, we discuss data demonstrating the existence of specialized Treg and therefore arguing against the validity of the first two postulates. However, based on the reactive nature of the immune system, we agree with Rolf's third postulate in that Treg cannot know ahead of time an ideal set-point for immune homeostasis.

A biological context for the self-nonself discrimination and the regulation of effector class by the immune system

An effective immune response to an antigen requires two sets of decisions: Decision 1, the sorting of the repertoire, and Decision 2, the regulation of effector class. The repertoire, because it is somatically generated, large, and random, must be sorted by a somatic mechanism that subtracts those specificities (anti-self) that, if expressed, would debilitate the host, leaving a residue (anti-nonself) that, if not expressed, would result in the death of the host by infection. The self-nonself discrimination is the metaphor used to describe Decision 1, the sorting of the repertoire. In order to be functional, the sorted repertoire must be coupled to a set of biodestructive and ridding effector functions, such that the response to each antigen is treated in a coherent and independent manner. Although a reasonably complete framework for Decision 1 exists, Decision 2 lacks conceptualization. The questions that must be considered to arrive at a proper framework are posed. It should be emphasized that manipulation at the level of Decision 2 is where clinical applications are likely to be found.

Does the signal for the activation of T cells originate from the antigen-presenting cell or the effector T-helper?

The present view is that the antigen-presenting cell (APC) processes and presents simultaneously on its surface several different antigens that are displayed randomly (with respect to their being Self or Nonself) as peptide-MHC complexes. The naive T-cell interacting with its ligand on the APC is activated by "co-stimulation," the first step on the pathway to effectors. This view ignores the requirement for associative recognition of antigen (ARA) in mediating both the Self-Nonself discrimination and the regulation of effector class. The introduction of ARA as a requirement for these two decision functions highlights a critical role for the effector T-helper (eTh) and necessitates rethinking the contribution of the APC.

On ‘Credo 2004’ as Viewed Under the ‘Development-Context’ Model of Colin Anderson

In analysing the Zinkernagel and Hengartner's 'Credo 2004,' Anderson introduces his 'development-context model' for the immunity-tolerance discrimination. He compares this model with the 'geographical model of Credo 2004' and our 'time-based two-signal model'. The discussion here deals with the advantages and limitations of the Anderson model considered largely at the level of principle. A meaningful discussion requires that we agree on the principle which separates the pathway of the effector output into two decision steps, the sorting of the repertoire and the regulation of effector class. The mechanism for the sorting of the repertoire is what might be referred to as the Self-Nonself discrimination. The black box approach, antigen-in, effector response-out, is what is referred to as the immunity-tolerance discrimination which includes the sorting of the repertoire. If this point of principle is accepted then we are left with a 'time-based two signal default model'.

What are the commonalities governing the behavior of humoral immune recognitive repertoires?

The humoral repertoire of immune systems is large, random and somatically selected. It is derived from a germline selected repertoire by a variety of diversification mechanisms, complementation of subunits, mutation and gene conversion. However derived, the end-product must be able to recognize and rid a vast variety of pathogens. This is accomplished by viewing antigens as combinatorials of epitopes, an astuce that permits a small repertoire to respond sufficiently rapidly to a vast antigenic universe. A somatically generated repertoire, however, requires a solution to two problems. First, a somatic mechanism for a self-nonself discrimination has to be put in place. Second, the repertoire has to be coupled to the effector mechanisms in a coherent fashion. The rules governing these two mechanisms are species-independent and delineate the parameters of all immune repertoires, whatever the somatic mechanism used to generate them.

A commentary on the Zinkernagel-Hengartner 'Credo 2004'

In 'Credo 2004', Zinkernagel and Hengartner give us a food-for-thought analysis of immune responsiveness based on a 'pragmatic and empiric point of view.' The Credo 2004 postulates derived by inductive extrapolation from observation to generalization do not satisfactorily account for immune behaviour because they lack a conceptualization as illustrated here. Nevertheless, Credo 2004 is certainly valuable in a limited framework because it is based on the most likely of assumptions namely that the immune system was evolutionarily selected to protect against infectious agents, and therefore the study of pathogens will most accurately reveal how the immune system responds normally to protect. After reformulating them, the postulates of Credo 2004 are analysed with respect to their generality.

The common sense of the self-nonself discrimination

The vertebrate immune system was evolutionarily selected to express a large random somatically generated paratopic repertoire coupled to effector mechanisms invented, in large measure, by non-vertebrates. The self-nonself discrimination is determined by Decision 1, the sorting of this repertoire into those specificities (anti-self) which, if expressed, would debilitate the host and those specificities (anti-nonself) which, if not expressed, would result in the death of the host by infection. Decision 1, the sorting of the repertoire, is mediated by a somatic learning process operating epitope-by-epitope that deletes anti-self specificities leaving the residue as anti-nonself. The activation of anti-nonself is the first step on entry into Decision 2, which optimizes the choice and magnitude of the effector class that rids the pathogen without significantly debilitating the host. The principles governing Decision 1, the self-nonself discrimination are analyzed here.

An alternative to current thinking about positive selection, negative selection and activation of T cells

Given that recognition by the T-cell receptor (TCR) of allele-specific determinants on major histocompatibility complex (MHC)-encoded restricting elements (Rs) is germline encoded, whereas recognition of peptide (P) is somatically encoded, two combining site repertoires, anti-R and anti-P, are implied. As a consequence, the three pathways of T cells, positive selection, negative selection and activation, must be signalled by qualitatively distinct interactions engaging the TCR. These are spelled out as they provide an alternative to the current thinking that these pathways depend on affinity-based quantitatively distinguishable interactions.

Whither T-suppressors: if they didn’t exist would we have to invent them?

Arriving at an understanding of the role of suppressor T-cells (regulatory T-cells, CD4(+)CD25+) depends on whether their functional repertoire is somatically selected to be anti-Self or anti-Nonself. Immunologists are ambivalent; often publications espousing opposite views share an author. Here the arguments are detailed that the suppressor repertoire is not somatically selected to be anti-Self, but rather it is anti-Nonself. Therefore, suppression cannot regulate the Self-Nonself discrimination; its function is to regulate the magnitude and class of the anti-Nonself effector response.

The heuristics of biologic theory: the case of self-nonself discrimination

Mel Cohn has responded to our critique of the minimal model of self-nonself discrimination proposed by Langman and him. In this response to Mel Cohn, we summarize the essential differences between our points of view and highlight one criterion (of many) for preferring one theory to another in the complex field of biology: a preferred theory, rather than solving a problem, is heuristic. A good theory is one that activates a scientist to perform experiments that are novel and productive.

A computerized model for the self-non-self discrimination at the level of the T(h) (Th genesis). II. The behavior of the system upon encounter with non-self antigens

In the final analysis, the self (S)-non-self (NS) discrimination is regulated by the sufficiency or insufficiency of effector T(h) (eT(h)) specific for the given antigen. We have described a model (Th genesis) for the origin of eT(h) based on an antigen-independent pathway from initial state T(h) (iT(h)) to eT(h), and on obligatory associative recognition of antigen (ARA) by an iT(h) and an eT(h) in order for the iT(h) to be activated. A computer analysis (referred to as Th genesis) was developed to evaluate this model that is extended here to describe the response to NS antigen. Th genesis fills in the missing element of the two-signal or ARA model for the S-NS discrimination, i.e. the origin of the primer eT(h). The conclusions from this analysis are compared with those of the other models for the origin of eT(h).

Does complexity belie a simple decision--on the Efroni and Cohen critique of the minimal model for a self-nonself discrimination

The immune system somatically generates a large and random paratopic repertoire that must be sorted into those specificities (anti-self) which, if expressed, would debilitate the host and those specificities (anti-nonself) which, if not expressed, would leave the host unprotected from infection. The critique of Efroni and Cohen that minimal models are misleading and without heuristic value is evaluated by illustrative examples.

Simplicity belies a complex system: a response to the minimal model of immunity of Langman and Cohn

Langman and Cohn have written a paper entitled "If the immune repertoire evolved to be large, random, and somatically generated, then em leader " This paper uses reductionist logic to prove that the minimal model of immunity proposed by Langman and Cohn is the only reasonable description of the workings of the immune system. Here we analyze the logic behind this model and show that the complexity of the real immune system contradicts the teachings of Langman and Cohn.