The common sense of the self-nonself discrimination

Heterologous humoral immunity to human and zoonotic coronaviruses: Aiming for the achilles heel

Coronaviruses are evolutionarily successful RNA viruses, common to multiple avian, amphibian and mammalian hosts. Despite their ubiquity and potential impact, knowledge of host immunity to coronaviruses remains incomplete, partly owing to the lack of overt pathogenicity of endemic human coronaviruses (HCoVs), which typically cause common colds. However, the need for deeper understanding became pressing with the zoonotic introduction of three novel coronaviruses in the past two decades, causing severe acute respiratory syndromes in humans, and the unfolding pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This renewed interest not only triggered the discovery of two of the four HCoVs, but also uncovered substantial cellular and humoral cross-reactivity with shared or related coronaviral antigens. Here, we review the evidence for cross-reactive B cell memory elicited by HCoVs and its potential impact on the puzzlingly variable outcome of SARS-CoV-2 infection. The available data indicate targeting of highly conserved regions primarily in the S2 subunits of the spike glycoproteins of HCoVs and SARS-CoV-2 by cross-reactive B cells and antibodies. Rare monoclonal antibodies reactive with conserved S2 epitopes and with potent virus neutralising activity have been cloned, underscoring the potential functional relevance of cross-reactivity. We discuss B cell and antibody cross-reactivity in the broader context of heterologous humoral immunity to coronaviruses, as well as the limits of protective immune memory against homologous re-infection. Given the bidirectional nature of cross-reactivity, the unprecedented current vaccination campaign against SARS-CoV-2 is expected to impact HCoVs, as well as future zoonotic coronaviruses attempting to cross the species barrier. However, emerging SARS-CoV-2 variants with resistance to neutralisation by vaccine-induced antibodies highlight a need for targeting more constrained, less mutable parts of the spike. The delineation of such cross-reactive areas, which humoral immunity can be trained to attack, may offer the key to permanently shifting the balance of our interaction with current and future coronaviruses in our favour.

Molecular pathobiology of scleritis and its therapeutic implications

Scleritis and other autoimmune diseases are characterized by an imbalance in the levels of pro-inflammatory and anti-inflammatory molecules with the balance tilted more towards the former due to the failure of recognition of self. The triggering of inflammatory process could be ascribed to the presence of cytoplasmic DNA/chromatin that leads to activation of cytosolic DNA-sensing cGAS-STING (cyclic GMP-AMP synthase linked to stimulator of interferon genes) pathway and enhanced expression of NF-κB that results in an increase in the production of pro-inflammatory bioactive lipids. Bioactive lipids gamma-linolenic acid (GLA), dihomo-GLA (DGLA), prostaglandin E1 (PGE1), prostacyclin (PGI2) and lipoxin A4, resolvins, protectins and maresins have anti-inflammatory actions, bind to DNA to render it non-antigenic and are decreased in autoimmune diseases. These results suggest that efforts designed to enhance the production of anti-inflammatory bioactive lipids may form a new approach to autoimmune diseases. Local injection or infusion of lipoxins, resolvins, protectins and maresins or their precursors such as arachidonic acid may be exploited in the prevention and management of autoimmune diseases including scleritis, uveitis and lupus/rheumatoid arthritis.

Exploring the elements for a successful immune offense against cancer

A successful immune attack on a tumor requires two elements. First, a nonself (NS) epitope that can act as an effective target must be expressed uniquely and uniformly on the tumor. Second, the immune system must be induced to produce an appropriate ridding effector activity specific for the cell expressing that de novo displayed NS-epitope. Today, the major effort is directed toward nonspecifically increasing the horsepower of the immune system by relieving suppressive and resistance factors using checkpoint blockade. This is coupled to the hope that the cancer will display a unique nonself determinant and that tolerance to Self (S) will not be abrogated. Here, these two elements will be explored in order to see what a more defined approach to the immune system treatment of cancer entails. While a Hail Mary approach may, in the end, be our only alternative, defining the elements of a solution, attainable or not, based on basic immunology, can only be salutary.

Core principles characterizing immune function

The immune system is an anticipatory mechanism designed by evolution to protect the individual against noxious agents and harmful cellular debris. In order to recognize substances that it has never encountered, the immune system somatically generates an appropriately sized random (with respect to self and nonself [NS]) recognitive repertoire that is coupled to a biodestructive and ridding output. Consequently, a Self-NS discrimination is required in order to avoid autoimmunity. This essay is an attempt to highlight the core principles upon which this anticipatory mechanism depends in order to function.

Analysis of Paris meeting redefining the "self" of the immune system

Some ideas because of their intuitive appeal never die by neglect and survive because they are not amenable to experimental disproof. They can only be evaluated by weighing them against competing ideas and by invoking a credibility factor when used to explain observation. Most scientists would recommend ignoring such ideas, yet there is much to be learned by engaging their proponents in debate. The immune system viewed as an idiotype network, and its tweaking by the new school of "contextualists" is an example of such an idea. As chance would have it, the supporters of this idea gathered in a meeting, thereby permitting a cumulative analysis of this conceptualization. The goal of this essay is to compare the views of each of the speakers in light of a competing theory with the hope that a better understanding of immune responsiveness will emerge.

Two unresolved problems facing models of the Self-Nonself discrimination

Although the Associative (linked) Recognition of Antigen (ARA) model for a Self (S)-Nonself (NS) discrimination, now over 50 years old, is built on a solid conceptual and experimental base, two unsettled questions remain. In examining these questions, unanticipated aspects of the ARA Model itself had to be reconsidered. This essay spells out these problems and suggests possible solutions.

What would Treg-cell biology look like when viewed from a rationalized perspective?

The argument that Treg cells play a role in determining the Self (S)-Nonself (NS) discrimination (i.e. tolerance) is challenged based on two theoretical constructs, the two stage-two signal model for the S-NS discrimination and the Tritope model of TCR function. The conclusions are then tested by reinterpreting a published probing set of data purporting to show that Treg cells regulate tolerance. It is concluded that the major role of suppression is to operate as a feedback mechanism modulating the magnitude of the effector response; it is not a determinant of the S-NS discrimination (i.e. tolerance).

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.

Conceptual aspects of self and nonself discrimination

Due to the variety and complexity of microorganisms, the mechanisms needed for pathogen recognition are diverse. Innate immune recognition is mainly based on a series of germ-line encoded receptors that have been selected by evolution to recognize nonself molecules present in microorganisms. Innate immunity also recognizes changes in our cells caused by infection, such as the lack or induction of self molecules. Adaptative immunity somatically generates large repertories of receptors which collectively recognize any nonself antigen. These receptors are randomly generated, and the adaptative immune system has to learn how to eliminate or inactivate cells with high avidity receptors for self molecules. Given the enormous variety of microbe structures and immune receptors, the difference between self and nonself is not absolute; it depends on the threshold of activation. In genetically diverse populations, individuals who have this activation threshold too far from the average may suffer an autoimmune reaction. Accumulation of mutations in cancer cells generates neoantigens that may be also recognized as nonself molecules, but the extent of self and nonself discrimination limits immune responsiveness to them. Surprisingly, most of the molecules expressed by cancer cells recognized by the immune system are non mutated self molecules.

The evolutionary context for a self-nonself discrimination

This essay was written to illustrate how one might think about the immune system. The formulation of valid theories is the basic component of how-to-think because the reduction of large and complex data sets by the use of logic into a succinct model with predictability and explanatory power, is the only way that we have to arrive at "understanding". Whether it is to achieve effective manipulation of the system or for pure pleasure, "understanding" is a universally agreed upon goal. It is in the nature of science that theories are there to be disproven. An experimentally disproven theory is a successful one. As they fail experimental test one by one, we end up with a default theory, that is, one that has yet to fail. Here, using the self-nonself discrimination as an example, how-to-think as I see it, will be illustrated.

Why Aire? Compensating for late bloomers

The question under analysis in this commentary is, what was the evolutionary selection pressure that necessitated the ectopic expression of a subset of peripheral self-antigens in the thymus and by peripheral APC? The suggestion is that antigen expression is delayed until after the immune system is responsive.

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.

How does the immune response get started?

An effective adaptive immune response requires the prior induction of the regulatory effector T-helper (eTh). There are two competing models of how this cell is induced to effectors. Under the Associative Recognition of Antigen (ARA) or "two signal" model, the T-helper requires eTh in order to be induced to eTh, an "autocatalytic" process. Under the "costimulation" model eTh are induced by an antigen-unspecific signal derived from an "activated" APC. Under the ARA model the problem of the origin of the primer eTh is posed. A nonself antigen-independent pathway to eTh is proposed as well as an experiment to reveal its existence. In the costimulation framework no primer eTh need be postulated but it lacks a mechanism that, in the absence of ARA, accounts for the self-nonself discrimination and the determination of effector class.

A rationalized set of default postulates that permit a coherent description of the immune system amenable to computer modeling

This discussion delineates and rationalizes a set of postulates that permit a coherent understanding of immune function. Although analytical tools such as mathematics and computer modeling have become very popular, simulation and data mining in the absence of a conceptual framework cannot increase understanding. The goal of this essay is to provide the foundation for a discussion that has as its goal the formulation of an agreed upon set of default postulates. Such a set is required to guide the algorithms needed to analyze complex immune behavior.

What roles do regulatory T cells play in the control of the adaptive immune response?

The immune system, like many systems responsive to specific stimuli, requires feedback regulation. The key regulatory element determining antigen-specific responsiveness is the effector T helper. As the response tends to overshoot, a feedback control of the magnitude of the response is critical to avoid immunopathology. This is the proposed role of the effector T suppressor (T(s)). The reasons for this interpretation of the data are discussed as are the reasons that the competing postulate is ruled out, namely that T(s) function in determining the self-non-self-discrimination. The regulatory T cell family consists of two lineages, T helpers and T(s). Differentiated derivatives of the T helper lineage drive the expression and amplification of specific classes of defensive effector cells. T(s) feedback to limit the magnitude of the process so that debilitating immunopathology is acceptably infrequent.

An in depth analysis of the concept of "polyspecificity" assumed to characterize TCR/BCR recognition

A workshop group developed the concept of a "polyspecific" TCR/BCR in the framework of today's consensus model. They argue that the individual TCR/BCR combining site is composed of a packet of specificities randomly plucked from the repertoire, hence it is "polyspecific." This essay analyzes the conclusions of the workshop and suggests an alternative. "Polyspecificity" must be dissected into its two component parts, specificity and degeneracy. The TCR and the BCR must be treated differently because the TCR recognizes allele-specifically the MHC-encoded restricting element (R) that serves as the platform presenting peptide (P). Only the anti-P paratope of the TCR behaves analogously to the BCR paratope. The two paratopes are selected to recognize a shape-determinant referred to as an epitope or ligand. The paratope is functionally unispecific in recognition, not polyspecific, with respect to shape; it is degenerate in recognition with respect to chemistry. The recognized shape-determinant can be the product of many chemically different substances, peptide, carbohydrate, lipid, steroid, nucleic acid, etc. Such a degenerate set is functionally treated by the paratope as one shape/epitope/ligand and, in no sense, can a paratope recognizing such a degenerate set be described as "polyspecific." Degeneracy and specificity are concepts that must be distinguished. The two positions are analyzed in this essay, the experiments used to support the view that the paratope of the TCR/BCR is polyspecific, are reinterpreted, and an alternative framework with its accompanying nomenclature, is presented.

T Cells Survey the Stability of the Self: A Testable Hypothesis on the Homeostatic Role of TCR-MHC Interactions

In the lifetime of an individual, every single gene will have undergone mutation on about 10(10) separate occasions. Nevertheless, cancer occurs mainly with advancing age. Here, we hypothesize that the evolutionary pressure driving the creation of the T cell receptor (TCR) repertoire was primarily the homeostatic surveillance of the genome. The subtly variable T cells may in fact constitute an evolutionary link between the invariable innate and hypervariable B cell systems. The new model is based on the homeostatic role of T cells, suggesting that molecular complementarity between the positively selected TCR and the self peptide-presenting major histocompatibility complex molecules establishes and regulates homeostasis, strictly limiting variations of its components. Notwithstanding, the 'homeostatic role of T cells' model offers a more realistic explanation as to how a naïve clonal immune system can cope with the much faster replicating pathogens, despite a limited repertoire that is capable of facing only a small fraction of the vast antigenic universe at a time.

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.

Tissue Homeostasis and Immunity – More on Models

This article continues the ongoing debate around models of the immune system. Earlier contributors have paid much attention to the various processes that lead to adaptive immune system aggression or tolerance. They have often based their discussions around facts that have been established by experimental investigation. However, both the observation and interpretation of these facts have been influenced by the function--or system goal--that is believed to have generated them. The perception of this function (of all or part of the immune system) is influenced by long established theories in immunology (e.g. horror autotoxicus, clonal deletion in utero, pathogen elimination, clonal selection, auto-immunity and so on) which, for many, have become enshrined as facts. One function that has had less consideration and has not been extensively investigated is the maintenance of tissue homeostasis. When the immune system is viewed from this perspective, the facts invite alternative interpretations. Whilst this perspective may not necessarily be the only valid one, let alone a correct one, viewing things this way--at least briefly--might help to expose hidden assumptions. It also emphasizes that the immune system is a system and, as such, it can by analysed through the principles of general systems theory.

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'.

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.