Overlap and Effective Size of the Human CD8+ T Cell Receptor Repertoire

Deep sequencing of the T cell receptor repertoires of seven healthy adults reveals that the adaptive immune system is far less diverse than expected and the person-to-person overlap is thousands of times larger. Not So Diverse After All You never know what nasty microbe lurks around the corner. To guard against these potential foes, our immune cells produce a vast variety of antibody and T cell receptor (TCR) shapes ready to recognize these pathogens. This diversity is manufactured by gene rearrangement, with fragments from the so-called V, D, and J gene groups joined together to form an array of sequences, much as colored beads can be arranged on a string to make many combinations. With several choices for each of the V, D, and J fragments, supplemented with a few random nucleotides inserted at the junctions, an astronomical number of different arrangements can theoretically be created. Originally, this was thought to be a random process, but Robins et al., by high-throughput genome sequencing of seven people, show that the generation of immune diversity is actually selective, creating an unexpectedly small assortment of TCRs that is similar in different people. By analyzing blood samples containing millions of T cells from healthy donors and sequencing the TCRs from each donor’s set of naïve and memory T cells, the authors revealed that the sequences of the TCRβ subunits in each subject are not randomly distributed. Instead, certain D and J segments preferentially associated with each other. The number of nucleotides inserted at junction sites between the segments was also smaller than expected. As a result, the actual repertoire of each person’s T cells is a fraction of that predicted by a computer model assuming random rearrangement, and the overlap between donors’ T cells is several orders of magnitude greater. If the rearrangements were truly random, two unrelated adults would only be expected to share on average five TCRβ sequences, of a total 3 million, but the overlap turned out to be more than 10,000 sequences. The authors also overturn another assumption in the field. It had been thought that a random set of V-D-J combinations was generated and then, by deletion and selection in the thymus of cells carrying less useful combinations, only a subset matured, forming the final immune repertoire. Instead, the authors show that the T cell repertoire is limited and biased from the time of the original V-D-J rearrangement during cell development. Now that deep sequencing of these key immune regions in individual genomes is achievable, we will be able to compare TCR sequences and antibodies in healthy individuals with those of patients with autoimmune disorders, or of transplant recipients suffering from graft-versus-host disease. The results may help to understand these illnesses and to look for ways to modify patients’ T cell repertoires for treatment or prevention of autoimmunity or to enhance compatibility between transplant donors and recipients. Diversity in T lymphocyte antigen receptors is generated by somatic rearrangement of T cell receptor (TCR) genes and is concentrated within the third complementarity-determining region 3 (CDR3) of each chain of the TCR heterodimer. We sequenced the CDR3 regions from millions of rearranged TCR β chain genes in naïve and memory CD8+ T cells of seven adults. The CDR3 sequence repertoire realized in each individual is strongly biased toward specific Vβ-Jβ pair utilization, dominated by sequences containing few inserted nucleotides, and drawn from a defined subset comprising less than 0.1% of the estimated 5 × 1011 possible sequences. Surprisingly, the overlap in the naïve CD8+ CDR3 sequence repertoires of any two of the individuals is ~7000-fold larger than predicted and appears to be independent of the degree of human leukocyte antigen matching.