A gain-of-function PIK3CD variant, R512W, impairs T cell function through polyamine-dependent metabolic dysregulation

We previously reported a patient harboring a novel heterozygous phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta (PIK3CD) missense variant (p.R512W) who presented with autoimmune features including Kawasaki disease, immune thrombocytopenic purpura, and systemic lupus erythematosus, without the classical signs of immunodeficiency typically associated with activated PI3Kδ syndrome (APDS). To elucidate the molecular mechanisms underlying this phenotype, we conducted functional and structural analyses of the R512W variant. Overexpression of mutant human p110δ (R512W) in a murine T cell line resulted in increased PIP3 accumulation and AKT phosphorylation, consistent with a gain-of-function effect. However, T cells expressing R512W exhibited paradoxical dysfunction, including reduced IL-2 production, impaired proliferation, increased PD-1 expression, and apoptosis, which are hallmarks of a T cell exhaustion-like state. A transcriptomic analysis revealed downregulation of polyamine biosynthesis genes, such as Odc1, Amd1, and Smox, along with reduced intracellular polyamine levels. Supplementation of the culture medium with spermidine partially rescued the proliferative defects, suggesting reversible metabolic insufficiency. Structural modeling indicated that R512W may alter the conformation of the helical domain of p110δ, potentially contributing to its hyperactivation. Unlike canonical APDS-associated mutations, the R512W variant appears to uncouple PI3K hyperactivation from effective T cell responses, resulting in immune dysregulation through both signaling and metabolic pathways. This autoimmune-dominant phenotype underscores mutation-specific clinical heterogeneity within the PIK3CD-associated disease spectrum. These findings reveal a novel link between aberrant PI3K signaling and polyamine metabolism, and suggest that targeting metabolic pathways may hold therapeutic potential in select cases of PI3K-driven autoimmunity.