PTPN22 mediates delayed negative feedback of T cell activation by forming an inhibitory signaling complex.

PTPN22 is a cytosolic tyrosine phosphatase expressed in immune cells that negatively regulates T cell receptor (TCR) signaling and implicated in autoimmune diseases through a common (R620W) variant. The molecular mechanisms by which PTPN22 modulates TCR activation remain incompletely understood. Here we show that upon T cell activation, PTPN22 forms delayed clusters at TCR microclusters (MCs) alongside Csk, STS-1 and PSTPIP, constituting a feedback inhibitory complex. Using imaging analyses, MS, and knockout mouse models, we demonstrate that this complex functions as a delayed negative regulation of TCR signaling, and that autoimmune-associated PTPN22 (R620W) mutant exhibits reduced binding to Csk and STS-1, impairing complex formation. Consequently, T cells expressing the mutant display enhanced cytokine production and immune responses. These findings reveal cooperative inhibitory mechanism involving PTPN22 and its partners that modulates T cell activation, providing insights into how PTPN22 variants contribute to autoimmune disease susceptibility.