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

Area of Science:

• Immunology
• Molecular Biology
• Genetics

Background:

• A patient with a novel PIK3CD missense variant (p.R512W) presented with autoimmune disorders but lacked typical immunodeficiency of Activated PI3Kδ Syndrome (APDS).
• Understanding the molecular basis of this autoimmune-dominant phenotype is crucial for defining the PIK3CD-associated disease spectrum.

Purpose of the Study:

• To investigate the functional and structural consequences of the PIK3CD R512W variant.
• To elucidate the mechanisms underlying the patient's autoimmune phenotype and T cell dysfunction.

Main Methods:

• Functional assays (PIP3 accumulation, AKT phosphorylation, IL-2 production, proliferation, PD-1 expression, apoptosis) in a murine T cell line overexpressing R512W.
• Transcriptomic analysis to identify affected cellular pathways.
• Structural modeling of the PIK3CD R512W variant.
• Polyamine level assessment and rescue experiments with spermidine.

Main Results:

• The R512W variant demonstrated gain-of-function activity, increasing PIP3 and AKT phosphorylation.
• Paradoxically, R512W-expressing T cells showed dysfunction, including reduced IL-2, impaired proliferation, increased PD-1, and apoptosis, resembling T cell exhaustion.
• Transcriptomics revealed downregulated polyamine biosynthesis genes and reduced polyamine levels, which were partially rescued by spermidine.
• Structural modeling suggested R512W alters p110δ conformation, potentially causing hyperactivation.

Conclusions:

• The R512W variant uncouples PI3K hyperactivation from effective T cell responses, leading to immune dysregulation via signaling and metabolic pathways.
• This highlights mutation-specific heterogeneity in PIK3CD-associated diseases, with an autoimmune-dominant presentation.
• Aberrant PI3K signaling and polyamine metabolism are linked, suggesting metabolic pathway targeting as a potential therapeutic strategy for PI3K-driven autoimmunity.