Novel PTPN2 Variants in Pediatric Patients with Autoimmune and Immunodeficiency Phenotypes: Functional Impact on STAT Signaling

Background Protein tyrosine phosphatase non-receptor type 2 (PTPN2) is a key negative regulator of the JAK/STAT pathway and is essential for immune homeostasis. Loss-of-function variants in PTPN2 have been implicated in monogenic autoimmunity. Case Series We identified novel heterozygous PTPN2 variants in three unrelated Argentinean pediatric patients presenting immune dysregulation. A patient with polyautoimmunity and polyinflammation was found to carry compound heterozygous variants c.515T>C (p.Ile172Thr) and c.865T>C (p.Trp289Arg), inherited from healthy heterozygous parents. In a second case, a child with Evans syndrome harbored the c.515T>C (p.Ile172Thr) variant. The third case involved a girl evaluated for recurrent bronchitis and diagnosed with an inborn error of immunity (IEI), carrying the c.865T>C (p.Trp289Arg) variant. Notably, her mother had previously been diagnosed with common variable immunodeficiency and died of gastric cancer. Methods To assess the functional consequences of these variants, we cloned wild-type (WT) PTPN2 cDNA into a mammalian expression plasmid with an HA-tag and introduced the two mutations via site-directed mutagenesis. HEK293T cells were transfected with WT/mutant PTPN2 constructs. Protein expression was evaluated by Western blot. Functional assays included co-transfection of PTPN2-HA constructs, WT-STAT3, and a STAT3-responsive GFP reporter, followed by IL-6 stimulation. Additionally, STAT1 activity was assessed using a STAT1-luciferase reporter system after IFN-γ stimulation. Results Mutant PTPN2 proteins were expressed at levels comparable to WT, suggesting preserved protein stability. However, cells expressing both PTPN2 variants (compound heterozygous state) showed significantly enhanced STAT3 activity upon IL-6 stimulation. STAT1 pathway analysis revealed altered luciferase activity in response to IFN-γ in cells transfected with each or both mutant constructs, suggesting broader dysregulation of JAK/STAT signaling. Conclusion These novel PTPN2 variants may contribute to immune dysregulation by enhancing STAT signaling. Functional evidence supports a pathogenic role consistent with the observed clinical phenotypes. Further studies are needed to define their contribution to autoimmunity and IEIs, and to explore therapeutic implications.