RESEARCH ARTICLE Early life imprints the hierarchy of T cell clone sizes Mario U Gaimann1,2, Maximilian Nguyen1, Jonathan Desponds3, Andreas Mayer1* 1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States; 2Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universita¨ t Mu¨ nchen, Mu¨ nchen, Germany; 3NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, United States Abstract The adaptive immune system responds to pathogens by selecting clones of cells with specific receptors. While clonal selection in response to particular antigens has been studied in detail, it is unknown how a lifetime of exposures to many antigens collectively shape the immune repertoire. Here, using mathematical modeling and statistical analyses of T cell receptor sequencing data, we develop a quantitative theory of human T cell dynamics compatible with the statistical laws of repertoire organization. We find that clonal expansions during a perinatal time window leave a long-lasting imprint on the human T cell repertoire, which is only slowly reshaped by fluctuating clonal selection during adult life. Our work provides a mechanism for how early clonal dynamics imprint the hierarchy of T cell clone sizes with implications for pathogen defense and autoimmunity. Introduction The hallmark of adaptive immunity is the generation of diversity through genetic recombination and clonal selection. Their interplay balances the breadth and specificity of the ~1012 T cells in the human *For correspondence: body (Figure 1A; Arstila et al., 1999; Farber et al., 2014): The genetic recombination of the T cell
[email protected] receptor (TCR) locus, termed VDJ recombination, generates an enormous potential diversity of receptors ranging from early estimates of ~1015 (Davis and Bjorkman, 1988) to more recent esti- Competing interests: The mates of ~1061 (Mora and Walczak, 2016) different possible receptor TCRab heterodimers.