Mus musculus strain:C57BL/6 Genome sequencing

T cell activation is a tightly controlled process that enables recognition of a remarkably broad range of antigens by the host repertoire without self-recognition leading to autoimmunity. Following recognition of cognate antigen, T cell costimulation represents a principal mechanism that regulates T cell activation. Immune checkpoint blockade therapy antagonizes negative costimulatory molecules such as CTLA-4 and PD-1. It remains unclear however, how loss of negative costimulation affects T cell differentiation. Here we comprehensively profile T cell populations that arise in the genetic absence of Ctla-4 or Pdcd-1. Loss of either of these negative costimulatory molecules leads to changes in the relative frequency of specific T cell subsets. In addition, loss of CTLA-4 and PD-1 leads to generation of non-canonical T cell subsets, indicating that negative costimulation normally acts to constrain T cell differentiation as well as attenuate T cell activation. Loss of CTLA-4 leads to the generation of multiple non-canonical CD4 T cell populations outside of the normal boundaries of T cell phenotypes. On the other hand, loss of PD-1 leads to the generation of a non-canonical CD8 T cell population. These findings indicate that loss of negative costimulation leads to fundamental defects in T cell differentiation, and furthermore, that CD4 and CD8 T cell differentiation are distinctly regulated by CTLA-4 and PD-1.