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

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.

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.

Ten experiments that would make a difference in understanding immune mechanisms

Jacques Monod used to say, "Never trust an experiment that is not supported by a good theory." Theory or conceptualization permits us to put order or structure into a vast amount of data in a way that increases understanding. Validly competing theories are most useful when they make testably disprovable predictions. Illustrating the theory-experiment interaction is the goal of this exercise. Stated bleakly, the answers derived from the theory-based experiments described here would impact dramatically on how we understand immune behavior.

Immune System as a Sensory System

As suggested by the well-known gestalt concept the immune system can be regarded as an integrated complex system, the functioning of which cannot be fully characterized by the behavior of its constituent elements. Similar approaches to the immune system in particular and sensory systems in general allows one to discern similarities and differences in the process of distinguishing informative patterns in an otherwise random background, thus initiating an appropriate and adequate response. This may lead to a new interpretation of difficulties in the comprehension of some immunological phenomena.

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.

Bridging innate and adaptive antitumor immunity targeting glycans

Effective immunotherapy for cancer depends on cellular responses to tumor antigens. The role of major histocompatibility complex (MHC) in T-cell recognition and T-cell receptor repertoire selection has become a central tenet in immunology. Structurally, this does not contradict earlier findings that T-cells can differentiate between small hapten structures like simple glycans. Understanding T-cell recognition of antigens as defined genetically by MHC and combinatorially by T cell receptors led to the “altered self” hypothesis. This notion reflects a more fundamental principle underlying immune surveillance and integrating evolutionarily and mechanistically diverse elements of the immune system. Danger associated molecular patterns, including those generated by glycan remodeling, represent an instance of altered self. A prominent example is the modification of the tumor-associated antigen MUC1. Similar examples emphasize glycan reactivity patterns of antigen receptors as a phenomenon bridging innate and adaptive but also humoral and cellular immunity and providing templates for immunotherapies.

How do regulatory T cells work?

CD4⁺ T cells are commonly divided into regulatory T (Treg) cells and conventional T helper (Th) cells. Th cells control adaptive immunity against pathogens and cancer by activating other effector immune cells. Treg cells are defined as CD4⁺ T cells in charge of suppressing potentially deleterious activities of Th cells. This review briefly summarizes the current knowledge in the Treg field and defines some key questions that remain to be answered. Suggested functions for Treg cells include: prevention of autoimmune diseases by maintaining self-tolerance; suppression of allergy, asthma and pathogen-induced immunopathology; feto-maternal tolerance; and oral tolerance. Identification of Treg cells remains problematic, because accumulating evidence suggests that all the presently-used Treg markers (CD25, CTLA-4, GITR, LAG-3, CD127 and Foxp3) represent general T-cell activation markers, rather than being truly Treg-specific. Treg-cell activation is antigen-specific, which implies that suppressive activities of Treg cells are antigen-dependent. It has been proposed that Treg cells would be self-reactive, but extensive TCR repertoire analysis suggests that self-reactivity may be the exception rather than the rule. The classification of Treg cells as a separate lineage remains controversial because the ability to suppress is not an exclusive Treg property. Suppressive activities attributed to Treg cells may in reality, at least in some experimental settings, be exerted by conventional Th cell subsets, such as Th1, Th2, Th17 and T follicular (Tfh) cells. Recent reports have also demonstrated that Foxp3⁺ Treg cells may differentiate in vivo into conventional effector Th cells, with or without concomitant downregulation of Foxp3.

On the sorting of the repertoire: an analysis of Cohn's challenge to integrity (Dembic), Round 2

In analyzing the integrity model and other context-based models, Melvin Cohn excluded the possibility that regulatory T cells or germline selected mechanisms can contribute to defining the specificity of immune responses. Here I discuss in greater detail how both the experimental data and a quantitative view of the evolution of immune control mechanisms challenge Cohn's arguments.

On the critique by Colin Anderson of 'A reply to Dembic: on an end to the beginning of mis-understanding the immune response'

My proposal of a set of postulates that can be used to guide computer modeling has understandably met with significant criticism at two levels, semantic and conceptual. The major source of contention is my assumption that the sorting of the paratopic repertoire is both necessary and sufficient to explain the evolutionarily selected mechanism for the self-nonself discrimination. While 'necessary' is agreed upon, 'sufficient' is debatable as this commentary illustrates. My essay is in defense of 'sufficiency'.

Placing regulatory T cells into global theories of immunity: an analysis of Cohn's challenge to integrity (Dembic)

In broadening the integrity model, Zlatko Dembic provided one of the few plausible explanations for the existence of regulatory T cells that has been postulated to date and at the same time highlighted deficiencies of the associative antigen recognition model. In defending the virtues of associative antigen recognition, Melvin Cohn has challenged the integrity model and the concept that regulatory T cells have a role in defining the specificity of immune responses. The critique of Cohn's analysis I present here suggests that a greater consideration of quantitative evolutionary constraints removes most of the challenges to integrity.

A reply to Dembic: on an end to the beginning of misunderstanding the immune response

We all agree that dealing with the complexity and volume of the data necessitates the use of computer modelling. This in turn requires a heuristic conceptual framework to guide this modelling. The first attempt to do this by Cohn has been criticized by Dembic as being severely lacking. This commentary deals with his criticism of the framework to show why Cohn's postulates, in fact, remain unchallenged.

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.