RT Journal Article
SR Electronic
T1 Mouse T cell repertoires as statistical ensembles: overall characterization and age dependence
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 086884
DO 10.1101/086884
A1 Zachary Sethna
A1 Yuval Elhanati
A1 Crissy S. Dudgeon
A1 Curtis G. Callan, Jr.
A1 Arnold Levine
A1 Thierry Mora
A1 Aleksandra M. Walczak
YR 2016
UL http://biorxiv.org/content/early/2016/11/10/086884.abstract
AB The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors (TCRs). This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts each time a new immune cell is created from a stem cell. By analyzing T cell sequence repertoires taken from the blood and thymus of mice of different ages, we quantify the significant changes in this process that occur in development from embryo to young adult. We find a rapid increase with age in the number of random insertions in the VDJ recombination process, leading to a dramatic increase in diversity. Since the blood accumulates thymic output over time, blood repertoires are mixtures of different statistical recombination processes and, by unraveling the mixture statistics, we can obtain a clear picture of the time evolution of the early immune system. Sequence repertoire analysis also allows us to detect the effect of selection on the output of the VDJ recombination process. The effects we find are nearly identical between thymus and blood, suggesting that they mainly reflect selection for proper folding of the TCR receptor protein.