Reading the adaptive receptor repertoires
Keywords: Immunology.

We humans evolve slower than our pathogens. It is the cost of multicellular bodies and long lifespans: how to survive to reproductive age while under continuous siege by viruses and bacteria that can mutate and divide in as little as 30 minutes? To keep up against this ever-changing sea of foes, our bodies produce a special class of remarkably diverse cells: our T and B lymphocytes. As each individual B and T cell matures, it uses specialized genomic shuffling machinery to generate a unique random receptor. Collectively, this results in an army of over 100 million unique B cell receptors and T cell receptors displayed across all of our lymphocytes: the adaptive immune receptor repertoire. The repertoire functions as a pattern recognition system, able to bind to and respond to nearly any pathogen or protein surface. It operates through brute force: by having hundreds of millions of unique receptors, the body will almost always have some with shape complementary to any molecular surface. While this extraordinary diversity is central to our ability to fend off pathogens, it has also made the adaptive immune system unusually difficult to study. In the history of immunology, every step to characterize these immune receptors, from their isola- tion, to their genomic locus sequencing, to solving their crystal structures, have been confounded by the underlying universe of variation. Even now, although a history of every immunological battle we have experienced is pumping through our veins, it has remained tantalizingly out of reach for routine inspection. As a consequence, the underlying etiologies of many immune-mediated diseases remain unresolved, and the molecular details of adaptive immune recognition are only partially characterized in almost all adaptive immune responses. Here we present a means of decoding the adaptive repertoire. We begin in chap- ter 1 by presenting the development of a series of enabling technologies for analyzing adaptive immune interfaces. Based on high-throughput sequencing, these technolo- gies allow millions of datapoints to be collected for B cell receptors, T cell receptors, single-cell paired heterodimer sequencing, high dimensional association of phenotypes, high-throughput HLA genotyping, and peptide-MHC complexes: all of the core in- teracting components of the adaptive immune repertoire. In chapter 2, we introduce convergence analysis: a statistical framework for identifying receptors and cells that perform a common function with non-identical but similar bits. We demonstrate that across αβ TCRs, γδ TCRs, BCRs, pMHC pools and phenotypes, convergence analysis provides a unifying framework for interpreting the adaptive immune system, and any degenerate system where combinatorial diversity exceeds functional diversity. In chapter 3, we review the consequences of clonal analysis and convergence groups on the relationship between genetics, environment, and random chance in the reper- toire's ability to form specific clones and shared specific responses to common immune stimulation. In chapter 4, a series of studies are presented that illustrate many of the findings that are being made possible by reading the repertoires. In chapter 5, we review interventional studies of selection pressures in the adaptive repertoire that are made evident through the construction of synthetic repertoires in controlled settings. In the final chapter, we comment on some of the new findings and new classes of research that can be anticipated based on these methods. Repertoire analysis is not a panacea. However, it will improve diagnostics by being able to rapidly identify thousands of reactivities by directly reading the BCR and TCR receptor repertoires. It will improve vaccine optimization by being able to rapidly assay relationships between changes in vaccine composition, and changes in number of clones, affinity of clones, isotype and addinity maturation of clones, and focus on different epitope targeting receptor groups that emerge in response. It will facilitate the rapid de-orphaning of antigen-specificities of TCRs in diseases of unknown cause. It may provide some benefit to discovery of therapeutically relervant receptors from natural responses, and guidance in further engineering of those recep- tors. Companioned with good experimental designs, it can further our understanding of the relationship between our genetics, our environment, and the random receptor generation engine inside of us.