PTPN2 deficiency: Amping up JAK/STAT

The JAK/STAT signaling pathway is responsible for transmitting signals from cytokine and growth factor receptors, with widespread functional consequences in immune and non-immune cells (Philips et al., 2022). Identification of germline and somatic monogenic defects that alter this pathway has provided insight into the role of JAK/STAT signaling in regulating the immune response in disease states, including in inborn errors of immunity (IEI) and malignancies (Toth et al., 2023). PTPN2 encodes a phosphatase responsible for the negative regulation of JAK/STAT signaling. Specifically, PTPN2 dephosphorylates JAK and STAT proteins, resulting in the cessation of STAT transcriptional activity and general dampening of inflammatory responses (Stanford and Bottini, 2023). Previous studies have identified germline heterozygous and homozygous variants in PTPN2 leading to loss-of-function (LOF) or haploinsufficiency of the encoded protein associated with autoimmune enteropathy (Awwad et al., 2023; Parlato et al., 2020), and in one family combined immunodeficiency and multi-organ autoimmunity (Thaventhiran et al., 2020). Jeanpierre et al. (2024) now identify novel germline heterozygous variants in PTPN2 in six patients with systemic autoimmunity, including systemic lupus erythematosus (SLE) and autoimmune cytopenias, and provide functional characterization demonstrating loss of regulatory function and enhanced cytokine signaling mediated by STATs in immune cells. These findings extend the range of known clinical phenotypes for PTPN2 deficiency and establish its association with monogenic lupus (Jeanpierre et al., 2024).

Jeanpierre et al. (2024) used whole exome sequencing to identify six unique PTPN2 variants in patients presenting with childhood-onset autoimmunity, with age of onset ranging from infancy to 9 years. One patient presented with childhood-onset SLE at age 5, with symptoms including rash, hematologic involvement, and nephritis. The remaining five patients were diagnosed with Evans syndrome, characterized by autoimmune hemolytic anemia and immune thrombocytopenia. Other clinical features included common variable immunodeficiency, recurrent infections, and lymphoproliferation. Of the genetic variants identified in PTPN2, two resulted in no detectable protein expression, whereas the other four resulted in reduced, but detectable, protein expression. Variants were functionally validated using a combination of primary cell assays and cell line models. Most variants that resulted in protein had reduced phosphatase activity as measured by dephosphorylation of STAT1 and STAT3 peptides. Transfection studies in cell lines demonstrated that all but one expressed PTPN2 variant had decreased ability to inhibit JAK/STAT signaling compared with wildtype. Stimulation of patient whole blood with IL-2 demonstrated increased phosphorylation of STAT5 in CD4 T cells and CD8 T cells, and IFN-γ stimulation led to increased phosphorylation of STAT1 in monocytes, while activated and cultured T cells also had delayed STAT5 dephosphorylation after IL-2 stimulation. Overall, these studies demonstrate impaired PTPN2 phosphatase activity in primary patient samples. Immune phenotyping by mass cytometry revealed variable changes including decreased numbers of natural killer cells and expanded CXCR5⁺ T follicular helper-like cells (Tfh) and CD11c⁺ B cells, including double negative (CD27⁻IgD⁻CD11c⁺) and activated naïve (CD27⁻IgD⁺CD11c⁺) B cells. Expansions of Tfh and CD11c⁺ B cells are consistent with immunophenotyping seen in other autoimmune conditions, including SLE and rheumatoid arthritis.

PTPN2 haploinsufficiency is part of a growing group of IEI that lead to enhanced JAK/STAT signaling (see figure) and immune dysregulation presenting clinically with autoimmunity, lymphoproliferation, autoinflammation and/or atopy (Tangye et al., 2022). These include gain-of-function (GOF) variants in genes encoding STATs (STAT1, 2, 3, 4, 5B, 6) and JAK1, and LOF variants in genes encoding regulators of JAK/STAT signaling (USP18, ISG15, SOCS1, PTPN2) (Baghdassarian et al., 2023; Jeanpierre et al., 2024; Toth et al., 2023). Serum cytokine profiles from patients with PTNP2 LOF resembled those seen in patients with STAT1 GOF and SOCS1 haploinsufficiency, demonstrating immunophenotypic overlap in these JAK/STAT disorders. Discovery of these monogenic diseases highlights the tight regulation of the STAT signaling pathway necessary to prevent breaches in tolerance and autoimmunity in human immunity, and the non-redundant pathways utilized to counter-regulate STAT activation. For example, SOCS1 is induced by signaling through multiple STATs, and binds to JAK1, JAK2, and TYK2 and prevents phosphorylation. PTPN2 plays a complementary inhibitory role by dephosphorylating JAKs and STATs to prevent continued activation of this pathway. USP18 is upregulated by type I IFNs and interacts with STAT2 to negatively regulate type I IFN receptor signaling, while ISG15 binds and stabilizes USP18. LOF in either of these leads to increased type I IFN signaling and autoinflammation, as well as susceptibility to infection (Martin-Fernandez et al., 2022).

In addition to identifying a new disease association, this study also illustrates the complexities of assigning pathogenicity to novel genetic variants in patients with IEI, including incomplete penetrance, the need for functional validation, and extending clinical phenotypes for new variants in genes previously associated with a disease. Three families had incomplete penetrance, genetic information from two families was not able to be obtained to determine segregation, and the final patient had a de novo variant in PTNP2. An increasing number of IEI are discovered with incomplete penetrance, particularly in the autosomal dominant state (Gruber and Bogunovic, 2020). Multiple mechanisms might explain incomplete penetrance in monogenic disorders, including the severity of the genetic defect, epistatic interactions with other genes, environmental exposures, mosaicism, and epigenetic mechanisms modulating expressivity (Kingdom and Wright, 2022). Incomplete penetrance also appears more common in cases of haploinsufficiency, presumably due to partial gene function from the unaffected allele. For example, variants in SOCS1 also result in incomplete penetrance (Hadjadj et al., 2020) similar to that seen here with PTPN2 haploinsufficiency. Incomplete penetrance presents difficulties for clinicians in ascribing pathogenicity, particularly when clinical phenotype does not match previously reported phenotypes and/or inheritance patterns for that gene. In these cases, rigorous functional studies to determine whether there is altered function of the encoded protein consistent with the immunologic phenotype are particularly important.

While prior patients with PTPN2 deficiency had immune dysregulation, the clinical phenotypes of SLE and autoimmune cytopenias were not prominent. This is often seen when new IEI are discovered in single cases or small cohorts, and expanding our understanding of the range of clinical presentations is important for clinicians interpreting genetic testing results and caring for these patients. JAK/STAT GOF disorders have a particularly broad phenotype, which has become evident with the characterization of large patient cohorts. For example, STAT1 GOF was initially identified in patients with susceptibility to mycobacterial infection, but careful clinical characterization of a large cohort identified that at least a third of patients have significant autoimmunity, including SLE as well as endocrinopathy and other symptoms (Toubiana et al., 2016). The first report of STAT3 GOF syndrome was based on discovery in a cohort of infants with neonatal onset type I diabetes mellitus (DM) (Flanagan et al., 2014), while a decade later, experience with a large cohort demonstrates a broad phenotype of early-onset lymphoproliferation and autoimmunity, with type I DM in ∼13% of cases and not limited to neonates (Leiding et al., 2023). There has been increasing recognition of the importance of genetic testing for patients with autoimmune disorders, particularly those with early-onset and/or unusual features. For patients and clinicians, the significance of these discoveries includes the potential to employ precision therapies. In patients with immune dysregulation due to JAK/STAT GOF syndromes, JAK inhibitors have been reported to have some success in individual cases but have not been tested in a larger clinical trial. Jeanpierre et al. (2024) tested the effects of the JAK1/3 inhibitor tofacitinib on cytokine-induced T cell proliferation using samples from patients with PTNP2 haploinsufficiency, which led to normalization of the proliferative phenotype. While it is interesting to hypothesize that this therapy would be of benefit to these patients, challenges include off-target effects, for example, inhibition of JAK/STAT signaling needed for other immune cell functions, and incomplete inhibition of altered signaling pathways.

Overall, identification of patients with PTPN2 haploinsufficiency stresses the importance of this pathway in regulating JAK/STAT signaling in the human immune response and establishes a new disease association with systemic autoimmunity. As this group of monogenic diseases with dysregulated JAK/STAT signaling grows, the next major hurdle and opportunity is to translate our mechanistic understanding of altered immune cell signaling to therapy for these patients.