Rationale

The capacity to mount an immune response is essential for the survival of organisms, as demonstrated by the fatal outcome of immunodeficiency syndromes, genetic or acquired. No antibiotic treatment can circumvent the lack of a functional immune system. However, the immune system might fail to protect the organism. Sometimes the cause of failure is an inappropriate handling of pathogens, some other times the pathogens just act too fast. In either of these circumstances, the pathogens spread and cause damage before the immune system can initiate an efficient response. The response time of the immune system is thus of vital importance. It is essentially determined by the the frequency and efficacy of the responding cells. Given these considerations, we would expect that the immune system learns what pathogens look like, both in the evolution of the species, as well as during the immune responses that take place during the life time of an organism. Indeed, in all species in which an immune system has been described, we find gene libraries of immune receptors, as well as mechanisms, such as somatic mutation that diversify the immune receptors throughout the lifetime of an organism. Immune receptor libraries consist of gene fragments that are used in a mutually exclusive fashion on different cells. Thus, an organism possesses multiple genetically-encoded receptor fragments, which can evolve independently of each other. Being encoded in the genome, these immune receptor genes may be subject to optimization, through mutation and selection on the basis of the survival of the organism. Moreover, the immune system also learns while an immune response is happening. The immune receptor genes undergo targeted mutation and selection on the basis of binding to pathogens. Mutations that are introduced in the gene during this process only affect the individual immune cells (lymphocytes), and are not transmitted to the offspring.

We thus have a basic understanding of the mechanisms that create diverse immune receptors. This is, however, not sufficient. What is crucial for the success of an immune reaction is the presence of the right receptor with the right frequency at the time of the pathogenic challenge. We therefore need to understand the role that these different mechanisms play in creating the immune repertoire.

There are a number of constraints that the immune repertoire seems to obey. Probably the most puzzling one is that it has to be capable of recognizing a wealth of molecules. Although it is not known, it is believed that there are many more possible molecular shapes than there are immune receptors in the body. Many animal studies use artificially created molecules, absent from the environment in which the species evolved, and immune responses are induced by these molecules as well. This is not due to indiscriminate binding of immune receptors to any type of molecule. We know that only 1 in 10⁴-10⁵ lymphocytes in the body reacts to any given pathogen (1971). The second important constraint on the immune system is that it should not react to molecules normally present in the body. Such occurrences are rare, and constitute the domain of auto-immune disease.

The focus of my research has been to understand what and how the immune system can learn about its pathogenic environment. I investigated what the role of the immune receptor libraries might be, how they could maximize their responsivity to a very large pathogen universe, and how they would be affected by pathogen evolution. I then analyzed individual immune receptor sequences, looking for evidence that these sequences are evolvable under somatic hypermutation. I found that codon bias that enhances evolvability under somatic mutation is present in individual gene sequences from a variety of species. That is, while the mutation/selection process takes place during an immune response, the parts of the gene that encode the pathogen-binding region are more likely to undergo mutations which change the amino acid sequence. This is likely to increase the efficiency with which receptors with high specificity for the pathogen are generated. I went on to show that the observed efficiency of this process cannot be explained unless the lymphocytes go through a number of cycles of mutation-selection-expansion. Finally, I introduce methods for estimating mutation rates in a variety of biological systems. My goal was to be able to estimate the mutation rate of immune receptors during an immune response. However, the applicability of these methods for mutation rate estimation is considerable wider.

Infectious disease remains a considerable threat to human society. We witness the emergence of new infectious agents relatively often. The Influenza virus, which is responsible for the flu epidemics, is one of the better known of the evolving pathogens. Human immunodeficiency virus is a more recent acquaintance. What the universe of possible pathogens looks like is a mystery to us, and this situation is not likely to change any time soon. What we can do though, in the effort of preventing infectious disease, is to understand what the immune receptors recognize, how immune memory develops, and how it is affected by pathogen evolution. The following chapters summarize my attempts in this direction.