Two articles in this issue of Arthritis & Rheumatism (1,2) provide critical confirmation of the association between rheumatoid arthritis (RA) and a functional polymorphism located in the coding region of PTPN22, the gene that encodes the intracellular protein tyrosine phosphatase nonreceptor 22 (PTPN22; also known as Lyp, a lymphoid-specific phosphatase). This observation now stands as the most robust and reproducible genetic association with RA outside of the HLA region. It is especially satisfying that the PTPN22 620W variant also predisposes to a variety of other autoimmune disorders in addition to RA, lending strong support to the opinion that common mechanisms and common molecular pathways underlie these disorders. What is most important is that this discovery is clearly useful in the sense that it raises a host of intriguing questions. We know just enough about the function of PTPN22 to proceed immediately with a rich variety of new experimental approaches that will encompass biochemistry, cell biology, animal disease models, population genetics, and epidemiology.

The year 2004 was clearly a landmark in terms of PTPN22 and human autoimmune disease. In March 2004, using a candidate gene approach, Bottini et al (3) reported that the minor allele (T) at nucleotide 1858 of PTPN22 confers a predisposition to type 1 diabetes in US and Italian populations. This polymorphism results in a substitution of tryptophan (W) for arginine (R) at codon 620 of the PTPN22 protein. Working independently and combining a broad screen of functional single-nucleotide polymorphisms guided by previously published linkage studies, Begovich et al (4) reported a similar association with RA, in the summer of 2004. These studies were followed by several confirmations of the PTPN22 association with type 1 diabetes (5–7) as well as convincing associations with systemic lupus erythematosus (8), Graves' disease, and Hashimoto thyroiditis (9, 10). More recently, several confirmations of the RA association have been reported (11, 12).

The 2 independent studies in this issue of Arthritis & Rheumatism add important new observations concerning the association of the PTPN22 620W allele with RA in several Canadian (1) and New Zealand (2) populations. Both studies confirm that the 620W allele confers a risk for RA of ∼1.5–2.0. In addition, these studies demonstrated that with the exception of one of the Canadian populations, homozygosity for the 620W variant more than doubles this risk, which is consistent with previous reports (4, 11, 12). Thus, overall, there is convincing evidence of a dose effect in disease susceptibility.

In both the study by van Oene and colleagues and that by Simkins et al, the association with PTPN22 extends to both rheumatoid factor–positive and rheumatoid factor–negative patients. This result is of interest because it contrasts with previous reports suggesting that the association is primarily with seropositive disease (4, 12). This discrepancy may reflect heterogeneity in the clinical populations or differences in other background genes in these populations. In general, the presence of autoantibodies is a prominent feature of the autoimmune diseases that have been associated with PTPN22. It will therefore be of great interest to determine whether the PTPN22 620W allele is associated with the presence of anti–citrullinated peptide antibodies in the setting of RA, which is a topic that has not yet been thoroughly addressed.

Importantly, despite the association of PTPN22 with the multiple different autoimmune disorders discussed above, there are some autoimmune diseases in which PTPN22 does not appear to play a role in susceptibility. One of these diseases is multiple sclerosis (13). The study by van Oene et al now extends these negative data to Crohn's disease. Autoantibodies are not a prominent feature of either of these disorders. In addition, results of studies in familial clustering of autoimmune disease suggest that the PTPN22-associated disorders (i.e., RA, type 1 diabetes, autoimmune thyroid disease, and lupus) may form a related group (10). In contrast, support is much more limited for clustering of multiple sclerosis and Crohn's disease with this group of disorders, although admittedly, the epidemiologic data are rather sparse. Given the fact that PTPN22 acts in part to regulate thresholds for T cell signaling (see below), these observations may lead to new insights into the different roles that T cells may play in these various disorders.

As noted above, PTPN22 belongs to a family of intracellular tyrosine phosphatases (14). It has been known for more than a decade that tyrosine phosphatase activity is associated with a negative regulatory effect on T cell function. Thus, early experiments showed that generalized phosphatase inhibition results in persistent proliferation of polyclonally activated T cells (15) or can induce spontaneous activation and cytokine release by resting T cells (16). A specific role of PTPN22 in T cell regulation has been confirmed by the results of knocking out the murine homolog of PTPN22 (PEST domain–enriched tyrosine phosphatase [PEP]), resulting in lowered thresholds for T cell receptor signaling in these animals (17). PEP-knockout mice on a nonautoimmune background (C57BL6) exhibit a variety of phenotypes consistent with T cell hyperresponsiveness, including enlargement of the spleen and lymph nodes due to T cell proliferation. This T cell proliferation becomes more prominent in older mice, with the spontaneous development of germinal centers that appear to be largely dependent on the enhanced T cell function present in the PEP−/− animals. Increased T cell proliferative capacity is primarily found within the effector/memory cell compartment in both CD4 and CD8 subsets and is accompanied by enhanced phosphorylation of activating tyrosine residues in both Lck and ZAP-70. Although there were increases in the levels of certain immunoglobulin isotypes in these knockout animals, autoantibodies did not develop, nor were there signs of overt autoimmune disease. Thus, PEP deficiency alone does not lead to clinical autoimmunity.

PTPN22 has been shown to bind to an intracellular tyrosine kinase, Csk. This binding occurs by virtue of a proline-rich SH3 binding site on PTPN22, interacting with the SH3 domain of Csk. As shown in Figure 1, these molecules act in concert to inactivate Lck, an Src family kinase that is involved in early T cell signaling events. Csk acts to phosphorylate tyrosine 505 (an inhibitory phosphate for Lck), while PTPN22 acts to remove the activating phosphate at tyrosine 394. The combined effect of these activities is to convert Lck to an inactive configuration (Figure 1).

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Figure 1. Regulation of the Lck activation state. Lck (green shading) is an Src family kinase involved in early T cell signaling events and is maintained in an inactive state in resting T cells by phosphorylation (P) of a C-terminal tyrosine 505 (Y505), as shown on the left side of the figure. The literature suggests that dephosphorylation of Y505 (possibly mediated by CD45) causes a conformational change in Lck, resulting in phosphorylation of an activating tyrosine residue Y394, leading to Lck activation, as shown at the right side of the figure. PTPN22 binds the tyrosine kinase Csk via a proline-rich SH3 binding site (P1). This binding is thought to enable colocalization of PTPN22 to Lck, dephosphorylation of Lck Y394, and return of Lck to an inactive state, with concomitant rephosphorylation of Y505 by Csk. TCR = T cell receptor; PAG = phosphoprotein associated with glycosphingolipid-enriched microdomains.

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The PTPN22 R620W polymorphism is located within the SH3 binding site of PTPN22. A tryptophan (W) substitution at this position has been shown to disrupt the binding of PTPN22 to Csk (3, 4). Thus, the disease-associated 620W allele is likely to cause changes in the regulation of Lck and result in loss of negative regulation of T cell receptor signaling. Clearly, this polymorphism does not completely eliminate the functions of PTPN22, because even homozygous carriers of PTPN22 620W do not exhibit a phenotype such as that of the knockout mouse. It is more likely that the 620W polymorphism results in a change in the level of effective PTPN22 activity in particular cell compartments. This view is supported by the dose effect that has been observed for the disease associations. Although reduction of PTPN22 has been shown to change thresholds for T cell receptor signaling in human cells (4), the functional effect of the PTPN22 620W allele on T cell function in humans has not yet been demonstrated. It is likely that sensitive assays will need to be developed to detect such threshold changes in signaling in primary human cells.

Although the currently available data suggest that PTPN22 acts primarily in T cells, it is now clear that this molecule is also expressed in other cell types, including B cells, monocytes, natural killer cells, and neutrophils (4, 18). In addition, although PTPN22 binds to the intracellular kinase Csk, there is also evidence that PTPN22 can bind to other proteins such as c-Cbl and Grb2 (18, 19). Baseline tyrosine phosphorylation is reduced in COS cells overexpressing Lyp/PEP, indicating that PEP may regulate the function of Cbl-associated proteins, such as ZAP-70 (20). Lyp also binds Grb2, a signaling adaptor molecule that is involved in CD28-mediated costimulation and T cell activation (19). Clearly, the full range of functions of PTPN22 remain to be defined, in terms of both signaling pathways and the cell types in which they act. Indeed, there is now an explosion of interest in phosphatases as regulators of a wide variety of cellular functions (21). More than 100 different tyrosine phosphatases have been defined; this exceeds the number of tyrosine kinases (14). Although all of these molecules are likely to have interesting biologic effects (21), PTPN22 is now going to receive a high level of scrutiny, given its clear involvement in RA and other forms of autoimmunity.

Finally, as alluded to in the beginning of this editorial, the association of PTPN22 with autoimmunity was discovered by 2 separate experimental approaches: a candidate gene approach on the part of Bottini and colleagues, and a broader “discovery-driven” approach taken by Begovich et al. In general, candidate gene approaches can be frustrating because of the frequent lack of replication of initial positive results (22), related in part to publication bias as well as the tendency of investigators to perform preliminary studies that are statistically underpowered. Fortunately, this was clearly not the case for PTPN22. In contrast, discovery-driven approaches, based on genome-wide linkage or association, have the general problem of too many positive results, which need to be corrected for the simultaneous testing of multiple markers and then replicated (23). However, the confirmation of PTPN22 as a risk gene for RA is an important validation of the discovery approach to gene identification used by Begovich et al, based on combining both genome-wide linkage and association.

Other discovery platforms, such as gene expression by microarray, are also beginning to yield valuable information for understanding autoimmune diseases, best exemplified by the identification of an interferon “signature” in the peripheral blood of patients with systemic lupus (24–26). Similar studies of RA have yielded evidence of monocyte activation (27, 28) as well as other changes (29). It is currently unclear to what extent, if any, PTPN22 signaling pathways are reflected in these findings. Morley and colleagues (30) have elegantly demonstrated that, by combining genetic analysis with these various discovery platforms, one can gain new insights into the relationship between genes and gene expression patterns and, ultimately, phenotype. The identification of PTPN22 as an important risk gene for autoimmunity now provides for a more directed approach to using these powerful discovery-based technologies to understand the biology underlying complex autoimmune disorders.


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