The Two SH2 Domains of SHP-2 Bridge Two PD-1 Molecules Resulting in SHP-2 Activation and PD-1-Mediated Inhibition

Programmed cell death-1 (PD-1) is a checkpoint inhibitory receptor member of the B7-CD28 family, which promotes peripheral tolerance and restrains anti-viral and anti-tumor immunity. Although PD-1 blockade leads to durable clinical responses in a fraction of patients, the majority of patients display only transient responses, emphasizing the need for better understanding of the mechanism of PD-1-mediated T cell inhibition. In contrast to other CD28 family family members, which form disulfide-linked homodimers, PD-1 lacks the juxtamembrane cysteine residue responsible for homodimer formation and has been shown to exist as a monomer. The cytoplasmic tail of PD-1 has one immunoreceptor tyrosine-based inhibitory motif (ITIM), centered on Y223 residue, and one immunoreceptor tyrosine-based switch motif (ITSM), centered on Y248 residue. Mutational studies have shown that PD-1-mediated inhibition relies on the interaction of the ITSM with SHP-2 but the mechanism by which PD-1 induces SHP-2 activation is unknown. In this study we sought to determine how PD-1: SHP-2 interaction leads to inhibition of T-cell responses. SHP-2 contains a phosphatase (PTP) domain and two SH2 domains, N-SH2 and C-SH2. To determine whether PD-1 selectively interacts with a specific SH2 domain of SHP-2, we generated five different GST-fusion proteins in which GST was fused with either SHP-2 full length (FL), SHP-2-N-SH2, SHP-2-C-SH2, SHP-2-ΔN-SH2 (lacking the N-terminus SH2 domain) or SHP-2-PTP. Surprisingly, pull-down assays with GST-fusion proteins using lysates from primary human T cells or Jurkat T cell line revealed that PD-1 interacted with SHP-2 via both SH2 domains of SHP-2. Biacore assays confirmed that phosphorylated ITSM Y248 interacted with SHP-2 N-SH2 and C-SH2. To determine whether one of the SHP-2 SH2 domains might preferentially interact with PD-1 in live cells, we mutagenized the functional sites of the N-SH2 or C-SH2 domain at arginine R32 and R138, respectively, and transfected COS cells with cDNA of SHP-2 wild type or each SHP-2 SH2 mutant, together with PD-1 and the TCR proximal kinase Fyn, required for PD-1 phosphorylation and interaction with SHP-2. Immunoprecipitation and immunoblot assays showed that mutagenesis of either SH2 domain abrogated interaction of SHP-2 with PD-1 ITSM Y248, providing evidence that both SH2 domains of SHP-2 are involved in the interaction with PD-1. Because each PD-1 molecule has only one ITSM, these results indicate that SHP-2 interacts via its two SH2 domains with two PD-1 molecules. Assessment of PD-1: PD-1 dimer formation in live cells by split luciferase complementation, using NanoBiT proximity assays, showed that upon PD-1 phosphorylation, PD-1: PD1 interaction occurs only in the presence of SHP-2 with intact N-SH2 and C-SH2 domains. The SH2 domains of SHP-2 have a crucial and distinct role in regulating SHP-2 PTPase activity. In the absence of a tyrosine-phosphorylated binding ligand, N-SH2 is bound to the PTP domain leading to an auto-inhibitory closed conformation that blocks the PTP active site. Phosphorylation of Y542 in the SHP-2 C-terminus tail leads to intramolecular interaction of Y542 with the N-SH2 domain to relieve binding to PTP domain. Similarly, intermolecular interaction of the N-SH2 domain with specific phosphorylated ligands disrupts its PTP recognition surface reversing the auto-inhibitory conformation and activates the phosphatase. We determined that monomeric PD-1 ITIM-pY223 or ITSM-pY248 peptides did not activate the PTP. A dimeric phosphopeptide generated by covalent joining of two PD-1 ITSM-pY248 phosphopeptides with a linker that matches the distance between the binding sites of the two SHP-2 SH2 domains induced rapid activation of SHP-2. In contrast, similarly designed dimeric peptides joining either two PD-1 ITIM-pY223 or ITIM-pY223-and-ITSM-pY248 phosphopeptides did not activate PTP activity of SHP-2. The ability of PD1 ITSM-pY248 to induce SHP-2 activation was correlated with inhibition of antigen-mediated IL-2 production, which was abrogated when Y248 was mutagenized to phenylalanine. Our results reveal the geometry of PD-1: SHP-2 interaction that leads to SHP-2 activation and have implications for the development of PD-1-binding compounds to selectively suppress T cell responses by dimerizing PD-1 or enhance T cell responses by disrupting PD-1 dimerization and SHP-2 activation.