The phosphotyrosine phosphatase SHP2 promotes anergy in chronic lymphocytic leukemia

TO THE EDITOR:

Anergy describes a state of B-cell receptor activation that leads to survival but not to proliferation in chronic lymphocytic leukemia (CLL) cells, and a high proportion of anergic cells correlates with an indolent clinical course. To gain deeper insights into anergic and proliferative CLL signaling, we performed Src homology 2 (SH2) domain profiling of phosphotyrosine-dependent signaling networks in a cohort of 34 untreated CLL patients by using the SH2 domains CRK, EAT2, GRB2, Pi3K, PLCγ, GAPN, SHIP2, and SHP2 (supplemental Figure 1A, available on the Blood Web site).¹  This analysis revealed 4 signaling clusters that were clinically relevant, because patients grouped in clusters 1 to 3 (58.8%) showed significantly longer time to first treatment (TTFT) than those in cluster 4 (26.5%) (supplemental Figure 1B). A third group (14.7%) was only distantly related and showed high EAT2 SH2 binding activity. Of the applied SH2 domains, the phosphatase SHP2 mainly accounted for differences between clusters 1 to 3 and cluster 4 with more SHP2 binding sites correlating with longer TTFT as a surrogate marker for an indolent clinical course (clusters 1 to 3 have an SHP2 SH2 high signature; supplemental Figure 1B-C). This clinical correlation was reproducible in a second cohort of 40 CLL patients using only the SH2 domain of SHP2. Taken together, patients with an SHP2 SH2 high signature had a significantly longer TTFT in the overall cohort (Figure 1A-B), suggesting that signaling pathways involving SHP2 might contribute to CLL pathobiology and disease progression.

SHP2 is a phosphotyrosine phosphatase (PTP) encoded by the PTPN11 gene. Indeed, this PTP was expressed in virtually all CLL patients at varying levels of expression (supplemental Figure 2). However, SHP2 expression levels were not predictive for the SHP2 SH2 signature, suggesting that the activated phospho-tyrosyl bound forms rather than global protein levels (including the closed autoinhibitory conformation) were responsible for the clinical correlation. To substantiate this, we determined the phosphatase activity of SHP2 in primary CLL cells by using an assay based on 6,8 difluoro-4-methylumbelliferyl phosphate (supplemental Figure 3). Of note, only 4 of 20 available primary CLL samples showing the SHP2 SH2 high signature yielded sufficient SHP2 immunoprecipitate to be used in the phosphatase activity screen, but immunoprecipitations from 16 of 25 available samples showing the SHP2 SH2 low signature were successful. This result may be explained by significantly more competing binding sites for SHP2 in the SHP2 SH2 high cluster. In line with our hypothesis, the phosphatase activity screen of all available samples from the 2 clusters revealed a significantly increased phosphatase activity of SHP2 in CLL patients from the SHP2 SH2 high signature (Figure 1C-D).

To further decipher the molecular mechanisms underlying the SHP2 signature, we used an MEC-1 knockdown and overexpression model as well as an OSU-CLL overexpression model, assuming that the knockdown would mimic the SHP2 SH2 low signature whereas overexpression of this protein would increase the SHP2 activity thereby mimicking, at least in part, the SHP2 SH2 high signature. In line with our hypothesis, the knockdown of SHP2 did not result in any proliferative effects, because SHP2 levels were already low in the parental MEC-1 cell line (supplemental Figure 4A-B). In contrast, overexpression of SHP2, but not a phosphatase-dead SHP2 mutant, resulted in reduced proliferation (Figure 2A). We used PamGene kinase profiling as an unbiased approach to pin down potential signaling pathways in which SHP2 could be involved in CLL. Kinase profiling pointed at Ca²⁺ and MAPK signaling as differentially activated in SHP2 overexpressing versus control MEC-1 cells (supplemental Figure 5). This prompted us to analyze SHP2 involvement in pathological BCR signaling, since an increase in intracellular Ca²⁺ concentration and enhanced MAPK signaling is one of the major initial steps in B-cell activation upon BCR engagement. Interestingly, overexpression of functional SHP2 resulted in a subtle increase of basal Ca²⁺ (Figure 2B) and MAPK signaling (Figure 2C) and in a downregulation of surface BCR (Figure 2D-E). Moreover, SHP2 overexpression mitigated responses to anti-immunoglobulin M (anti-IgM) stimulation such as Ca²⁺ mobilization as well as activation of downstream MAPK signaling (Figure 2F-G). Antiproliferative effects of ibrutinib were enhanced in MEC-1 cells overexpressing SHP2 (Figure 2H). Confirming the observations in the MEC-1 cell line model, reduced proliferation and Ca²⁺ mobilization were also observed in OSU-CLL cells overexpressing SHP2 in contrast to a phosphatase-dead mutant SHP2 (supplemental Figure 6A-B). However, these effects were smaller in comparison with the MEC-1 cell line model, which was presumably due to the low level of overexpression achieved in OSU-CLL and comparable, but very low, surface BCR expression between the different OSU-CLL sublines (supplemental Figure 6C-D).

The pattern of IgM downregulation with attenuated responses to BCR engagement along with enhanced basal MAPK signaling has been previously recognized as characteristic for anergic B cells.^2,3  Anergy is one of the most important physiological mechanisms to silence autoreactive B cells.⁴  Whereas in normal B cells, this program leads to apoptosis in the long term,⁵  in CLL cells, it seems to result in lethargic survival without proliferation as a result of widespread overexpression of the anti-apoptotic protein BCL-2 in this disease.^6,7  Conceptually, anergy may seem to be more desirable, and indeed a high proportion of anergic cells is correlated with an indolent clinical course in this disease.⁸  Yet anergy describes a functional rather than an irreversible state of the cell, and therefore anergic cells are potentially harmful if they ultimately re-enter the proliferative cycle.^9,10  Such recirculating cells re-express high levels of surface IgM, show strong inducible anti-IgM responses, engage T-cell help, and ultimately proliferate in lymph node proliferation centers. The balance between positive signaling that leads to proliferation and negative signaling that leads to anergy is therefore of prognostic significance in CLL.^9,11 

Although the cellular hallmarks of anergy are well established, the molecular drivers of this signature have been insufficiently elucidated so far. Previous experiments showed that SHIP1 and SHP1 (2 downstream phosphatases of Lyn acting in parallel pathways) were found to be important for maintaining the anergic state in B cells.¹²  One underlying mechanism could be the dephosphorylation of PIP3 by SHIP1 and PTEN that antagonizes PI3K signaling.¹³  In line with this, a subset of anergic B cells seems to overexpress PTEN.¹⁴  The SHP1 phosphatase plays a role in anergic feedback inhibition downstream of the BCR, but recent evidence suggests that it plays a much more complex role in CLL as part of the signalosome that orchestrates survival signals.¹⁵  Although anergic CLL cells do show significantly enhanced ERK1/2 phosphorylation,¹⁶  previous work failed to identify the link between BCR pathway attenuation and MAPK signaling. The data presented here indicate that SHP2 may serve as a molecular regulator of anergy in CLL and may be the missing link between attenuated responses to BCR stimulation and enhanced basal MAPK signaling as schematically shown in supplemental Figure 7. Importantly, our data clearly demonstrate that these effects are mediated by the phosphatase domain of SHP2, because a phosphatase-dead mutant of SHP2 did not induce an anergic phenotype. Taken together, our data broaden our understanding of pathological BCR signaling in CLL and may be exploited for therapeutic targeting.