SHP2 Mutants Research Articles

Previously Published Phosphatase Probes have Limited Utility Due to their Unspecific Reactivity.

This study explores the use of activity-based protein profiling to study protein tyrosine phosphatases. With the discovery of allosteric SHP2 inhibitors, this enzyme family has resurfaced as interesting drug targets. Therefore, we envisioned that previously described direct electrophiles and quinone methide-based traps targeting phosphatases could be applied in competitive activity-based protein profiling assays. This study evaluates three direct electrophiles, specifically, a vinyl sulfonate, a vinyl sulfone, and an α-bromobenzylphosphonate as well as three quinone methide-based traps as activity-based probes. For all these moieties it was previously shown that they could selectively engage in assays with purified or overexpressed phosphatases in bacterial lysates. However, this study demonstrates that probes based on these moieties all suffer from unspecific labelling. Direct electrophiles were either unspecific or not activity-based, while quinone methide-based traps showed dependence on phosphatase activity but also resulted in unspecific labelling due to diffusion after activation. This phenomenon, termed 'bystander' labelling, occurred even with catalytically inactive SHP2 mutants. We concluded that alternative strategies or chemistries are needed to apply activity-based protein profiling in phosphatase research. Moreover, this study shows that quinone methide-based designs have limited potential in probe and inhibitor development strategies due to their intrinsic reactivity.

Bivalent target-binding bioPROTACs induce potent degradation of oncogenic SHP2

Targeted protein degradation is an emergent and rapidly evolving therapeutic strategy. In particular, biologics-based targeted degradation modalities (bioPROTACs) are relatively under explored compared to small molecules. Here, we investigate how target affinity, cellular localization, and valency of bioPROTACs impact efficacy of targeted degradation of the oncogenic phosphatase src-homology 2 containing protein tyrosine phosphatase-2 (SHP2). We identify bivalent recruitment of SHP2 by bioPROTACs as a broadly applicable strategy to improve potency. Moreover, we demonstrate that SHP2-targeted bioPROTACs can effectively counteract gain-of-function SHP2 mutants present in cancer, which are otherwise challenging to selectively target with small molecule constructs. Overall, this study demonstrates the utility of bioPROTACs for challenging targets, and further explicates design principles for therapeutic bioPROTACs.

The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain

Mutations in the tyrosine phosphatase Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting autoinhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8 to 10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine-binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.

SHP2 mutations promote glycolysis and inhibit apoptosis via PKM2/hnRNPK signaling in colorectal cancer

Colorectal cancer (CRC) is one of the most common gastrointestinal tumors. Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) mutations occur in human solid tumors, including CRC. However, the function and underlying mechanism in CRC have not been well characterized. We demonstrated that the SHP2D61Y and SHP2E76K mutations occurred in CRC tissues, and these mutations promoted CRC cell proliferation, migration/invasion, and reduced CDDP-induced cell apoptosis invitro and invivo. Mechanistically, SHP2D61Y and SHP2E76K promote glycolysis by accelerating pyruvate kinase M2 (PKM2) nuclear translocation through mechanism beyond ERK activation. PKM2-IN-1 attenuates PKM2-dependent glycolysis and reduce glucose uptake, lactate production, and ATP levels promoted by SHP2D61Y and SHP2E76K in CRC cells. Furthermore, PKM2 upregulates heterogeneous nuclear ribonucleoprotein K (hnRNPK) expression and increases CRC cell proliferation and migration/invasion via regulating hnRNPK ubiquitination. These findings provide evidence that SHP2D61Y and SHP2E76K regulate CDDP-induced apoptosis, glucose metabolism, and CRC migration/invasion through PKM2 nuclear translocation and PKM2/hnRNPK signaling.

Computational study on the binding mechanism of allosteric drug TNO155 inhibiting SHP2E76A.

E76A mutations of SHP2 have been reported to associate with genetic developmental diseases and cancers, and TNO155 is one of the effective inhibitors targeted to the allosteric site 1, which has already entered the clinical stage. However, the detailed binding mechanism between them still needs further clarification at micro-atomic level. In this study, the binding mechanism of TNO155 inhibiting SHP2E76A and the superiorities of TNO155 at binding affinity and dynamic interactive behavior with SHP2E76A were probed utilizing a series of computational drug design technologies. The results show that SHP2E76A forms tighter interaction with TNO155 compared to SHP099. SHP2E76A-TNO155 exhibits the largest electrostatic interaction among all complex systems, which can be manifested by the strong hydrogen bond interactions formed by two electrically charged residues, Arg111 and Glu250. Notably, in SHP2E76A-TNO155 system, Asp489 makes an additional substantial beneficial contribution. The E76A mutation brings stronger residue positive correlation and a larger conformation fluctuation between N-CH2 and PTP domains, resulting in tighter binding betweenTNO155and SHP2E76A. This study offers valuable insights for the further design and development of novel SHP2E76A allosteric inhibitors.

SHP2-EGFR States in Dephosphorylation Can Inform Selective SHP2 Inhibitors, Dampening RasGAP Action.

SHP2 is a positive regulator of the EGFR-dependent Ras/MAPK pathway. It dephosphorylates a regulatory phosphorylation site in EGFR that serves as the binding site to RasGAP (RASA1 or p120RasGAP). RASA1 is activated by binding to the EGFR phosphate group. Active RASA1 deactivates Ras by hydrolyzing Ras-bound GTP to GDP. Thus, SHP2 dephosphorylation of EGFR effectively prevents RASA1-mediated deactivation of Ras, thereby stimulating proliferation. Despite knowledge of this vital regulation in cell life, mechanistic in-depth structural understanding of the involvement of SHP2, EGFR, and RASA1 in the Ras/MAPK pathway has largely remained elusive. Here we elucidate the interactions, the factors influencing EGFR's recruitment of RASA1, and SHP2's recognition of the substrate site in EGFR. We reveal that RASA1 specifically interacts with the DEpY992LIP motif in EGFR featuring a proline residue at the +3 position C-terminal to pY primarily through its nSH2 domain. This interaction is strengthened by the robust attraction of two acidic residues, E991 and D990, of EGFR to two basic residues in the BC-loop near the pY-binding pocket of RASA1's nSH2. In the stable precatalytic state of SHP2 with EGFR (DADEpY992LIPQ), the E-loop of SHP2's active site favors the interaction with the (-2)-position D990 and (-4)-position D988 N-terminal to pY992 in EGFR, while the pY-loop constrains the (+4)-position Q996 C-terminal to pY992. These specific interactions not only provide a structural basis for identifying negative regulatory sites in other RTKs but can inform selective, high-affinity active-site SHP2 inhibitors tailored for SHP2 mutants.

Abstract 6060: Discovery of potent SHP2 protein degraders with strong anti-tumor activities in KRAS mutant cancers

Abstract Background: SHP2 plays a pivotal role in modulating the RTK/RAS/MAPK signaling pathway, which is frequently dysregulated in various cancers. Multiple allosteric SHP2 inhibitors have been under active development for the treatment of RTK/RAS/MAPK-dependent cancers, while certain limitations have come to light, such as their inability to target the active form of SHP2 and narrow therapeutic index necessitating intermittent dosing to mitigate toxicity. To overcome these challenges, we have discovered SHP2 protein degraders as next generation SHP2 targeting agents. Here, we present compelling profiles of our SHP2 degraders. Methods: We employed a variety of cancer cell lines harboring mutations in RTK, KRAS, or SHP2 for assessing in vitro activity of SHP2 degraders. For in vivo assessment of pharmacological profile, we utilized an NCI-H358 KRAS G12C mutant NSCLC xenograft. SHP2 protein levels in cell lysates and tumors were analyzed to assess SHP2 degradation efficiency. Simultaneously, ERK phosphorylation and DUSP6 mRNA levels were analyzed to evaluate downstream effects. Immunoprecipitation assays were used to assess the impact on SHP2's scaffolding roles. Results: A series of SHP2 degraders have been identified, demonstrating highly efficient SHP2 degradation activity with DC50 values in subnanomolar ranges. Robust inhibition of ERK phosphorylation, followed by remarkable anti-cancer effects in multiple KRAS mutant cancer cell lines were observed. Interestingly, in vitro cell growth inhibition by SHP2 degraders are 10 times more potent than SHP2 inhibitors currently under clinical development. Further characterization reveals several advantages of SHP2 degraders compared to SHP2 inhibitors. First, we observed a more efficient disruption of SHP2 scaffolding function, such as the formation of the SHP2-GRB2-GAB1 complex. Second, we detected effective degradation of activating mutants of SHP2, such as E76K and T507K, which are typically not targeted by SHP2 inhibitors. Experiments using a KRAS mutant CDX model demonstrate compelling in vivo profiles. A single administration of lead compounds resulted in Dmax values exceeding 95% in tumors, accompanied by the significant reduction of downstream signaling markers, such as p-ERK and DUSP6 mRNA. Notably, the reduced levels of SHP2 and downstream markers persist for several days. This suggests that utilizing intermittent dosing could be a viable approach with SHP2 degraders. Once-weekly intravenous administration achieved strong tumor growth inhibition without causing significant body weight loss. Conclusion: We have successfully discovered novel SHP2 degraders exhibiting remarkable activities. We demonstrate that SHP2 degraders have potential to overcome the limitations associated with allosteric SHP2 inhibitors and provide a promising therapeutic option for RTK/RAS/MAPK-dependent cancer patients. Citation Format: So Hyun Kim, Jihye Lee, Jiyoung Song, Geon-Tae Park, Jieun Jung, Jungtae Na, Dong Ho Lee, Soohyun Lee, Ji Youn Park, Jiyoung Kim, Onnuri Bae, Jeonghwa Han, Ju Young Kang, Mijin Moon, Yongje Shin, Je Ho Ryu, Song Hee Lee, Sook-Kyung Park. Discovery of potent SHP2 protein degraders with strong anti-tumor activities in KRAS mutant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6060.

Galectin 7 leads to a relative reduction in CD4+ T cells, mediated by PD-1

The role of glycan-binding proteins as an activator of immune regulatory receptors has gained attention recently. We report that galectin 7 reduced CD4+ T cell percentage in both in vitro culture and mouse tumor models. Immunohistochemical staining of esophageal cancer patient samples showed a lower percentage of CD4+ cells in the galectin 7 high area. The lack of CD4+ T cell depletion by galectin 7 in PD-1 knockout mice supports the role of PD-1 in mediating the effects of galectin 7. The binding assays demonstrate that galectin 7 binds to the N-glycosylation of PD-1 on N74 and N116 sites and leads to the recruitment of SHP-2. NFAT suppressive activity of galectin 7 was abrogated upon overexpression of the dominant negative SHP-2 mutant or inhibition of PD-1 by siRNA. Glycosylation of PD-1 has been reported to play a critical role in surface expression, stability, and interaction with its ligand PD-L1. This report further expands the significance of PD-1 glycosylation and suggests that galectin 7, a glycan-binding protein, interacts with the immune regulatory receptor PD-1 through glycosylation recognition.

Discovery of 1H-pyrazolo[3,4-b]pyrazine derivatives as selective allosteric inhibitor of protein tyrosine phosphatase SHP2 for the treatment of KRASG12C-mutant non-small cell lung cancer

The high expression or mutation of SHP2 can induce cancer, so targeting SHP2 has become a new strategy for cancer treatment. In this study, we used the previously reported SHP2 allosteric inhibitor IACS-13909 as a lead drug for structural derivation and modification, and synthesized three SHP2 inhibitors. Among them, 1H-pyrazolo[3,4-b]pyrazine derivative 4b was a highly selective SHP2 allosteric inhibitor, with an IC50 value of 3.2 nM, and its inhibitory activity was 17.75 times than that of the positive control IACS-13909. The cell proliferation experiment detected that compound 4b would markedly inhibit the proliferation of various cancer cells. Interestingly, compound 4b was highly sensitive to KRASG12C-mutant non-small cell lung cancer NCI-H358 cells, with an IC50 value of 0.58 μM and its antiproliferative activity was 4.79 times than that of IACS-13909. Furthermore, the combination therapy of compound 4b and KRASG12C inhibitor sotorasib would play a strong synergistic effect against NCI-H358 cells. The western blot experiment detected that compound 4b markedly downregulated the phosphorylation levels of ERK and AKT in NCI-H358 cells. Molecular docking study predicted that compound 4b bound to the allosteric site of SHP2 and formed H-bond interactions with key residues Thr108, Glu110, Arg111, and Phe113. In summary, this study aims to provide new ideas for the development of SHP2 allosteric inhibitors for the treatment of KRASG12C mutant non-small cell lung cancer. Communicated by Ramaswamy H. Sarma

SHP2 clinical phenotype, cancer, or RASopathies, can be predicted by mutant conformational propensities.

SHP2 phosphatase promotes full activation of the RTK-dependent Ras/MAPK pathway. Its mutations can drive cancer and RASopathies, a group of neurodevelopmental disorders (NDDs). Here we ask how same residue mutations in SHP2 can lead to both cancer and NDD phenotypes, and whether we can predict what the outcome will be. We collected and analyzed mutation data from the literature and cancer databases and performed molecular dynamics simulations of SHP2 mutants. We show that both cancer and Noonan syndrome (NS, a RASopathy) mutations favor catalysis-prone conformations. As to cancer versus RASopathies, we demonstrate that cancer mutations are more likely to accelerate SHP2 activation than the NS mutations at the same genomic loci, in line with NMR data for K-Ras4B more aggressive mutations. The compiled experimental data and dynamic features of SHP2 mutants lead us to propose that different from strong oncogenic mutations, SHP2 activation by NS mutations is less likely to induce a transition of the ensemble from the SHP2 inactive state to the active state. Strong signaling promotes cell proliferation, a hallmark of cancer. Weak, or moderate signals are associated with differentiation. In embryonic neural cells, dysregulated differentiation is connected to NDDs. Our innovative work offers structural guidelines for identifying and correlating mutations with clinical outcomes, and an explanation for why bearers of RASopathy mutations may have a higher probability of cancer. Finally, we propose a drug strategy against SHP2 variants-promoting cancer and RASopathies.

Protein Tyrosine Phosphatase SHP2 in Macrophages Acts as an Antiatherosclerotic Regulator in Mice.

Macrophages have versatile roles in atherosclerosis. SHP2 (Src homology 2 containing protein tyrosine phosphatase 2) has been demonstrated to play a critical role in regulating macrophage activation. However, the mechanism of SHP2 regulation of macrophage function in an atherosclerotic microenvironment remains unknown. APOE (apolipoprotein E) or LDLR (low-density lipoprotein receptor) null mice treated with SHP099 were fed a Western diet for 8 weeks, while Shp2MKO:ApoE-/- or Shp2MKO:Ldlr-/- mice and exo-AAV8-SHP2E76K/ApoE-/- mice were fed a Western diet for 12 weeks. In vitro, levels of proinflammatory factors and phagocytic function were then studied in mouse peritoneal macrophages. RNA sequencing was used to identify PPARγ (peroxisome proliferative activated receptor γ) as the key downstream molecule. A PPARγ agonist was used to rescue the phenotypes observed in SHP2-deleted mice. Pharmacological inhibition and selective deletion in macrophages of SHP2 aggravated atherosclerosis in APOE and LDLR null mice with increased plaque macrophages and apoptotic cells. In vitro, SHP2 deficiency in APOE and LDLR null macrophages enhanced proinflammatory polarization and its efferocytosis was dramatically impaired. Conversely, the expression of gain-of-function mutation of SHP2 in mouse macrophages reduced atherosclerosis. The SHP2 agonist lovastatin repressesed macrophage inflammatory activation and enhanced efferocytosis. Mechanistically, RNA sequencing analysis identified PPARγ as a key downstream transcription factor. PPARγ was decreased in macrophages upon SHP2 deletion and inhibition. Importantly, PPARγ agonist decreased atherosclerosis in SHP2 knockout mice, restored efferocytotic defects, and reduced inflammatory activation in SHP2 deleted macrophages. PPARγ was decreased by the ubiquitin-mediated degradation upon SHP2 inhibition or deletion. Finally, we found that SHP2 was downregulated in atherosclerotic vessels. Overall, SHP2 in macrophages was found to act as an antiatherosclerotic regulator by stabilizing PPARγ in APOE/LDLR null mice.

Design, synthesis, activity and molecular dynamics studies of 1,3,4-thiadiazole derivatives as selective allosteric inhibitors of SHP2 for the treatment of cancer

Overexpression or gene mutation of SHP2 is closely linked with a variety of cancers and has been identified as a crucial anticancer target. In the study, we took SHP2 allosteric inhibitor SHP099 as the lead compound, and 32 1,3,4-thiadiazole derivatives were identified as selective allosteric inhibitors of SHP2. In vitro enzyme activity test showed that some compounds had high inhibition on full length SHP2, and almost no activity on homologous protein SHP1, exhibiting high selectivity. Compound YF704 (4w) had the best inhibition activity, with IC50 value of 0.25 ± 0.02 μM, and also showed strong inhibitory activity on SHP2-E76K and SHP2-E76A, with IC50 values of 6.88 ± 0.69 μM and 1.38 ± 0.12 μM, respectively. CCK8 proliferation test found that multiple compounds would effectively inhibit the proliferation of a variety of cancer cells. Among them, the IC50 values of compound YF704 on MV4-11 and NCI–H358 cells were 3.85 ± 0.34 μM and 12.01 ± 0.62 μM, respectively. Specially, these compounds were sensitive to NCI–H358 cells containing KRASG12C mutation, thus overcoming the problem that SHP099 was insensitive to such cells. Apoptosis experiment showed that compound YF704 would effectively induce apoptosis of MV4-11 cells. Western blot showed that compound YF704 would downregulate the phosphorylation levels of Erk1/2 and Akt in MV4-11 and NCI–H358 cells. Molecular docking study show that compound YF704 would effectively bind to the allosteric region of SHP2 and form hydrogen bond interactions with key residues Thr108, Arg111 and Phe113. Molecular dynamics study further revealed the binding mechanism of SHP2 and compound YF704. In conclusion, we hope to provide potential SHP2 selective inhibitors and provide valuable clues for cancer treatment.

In silico mutagenesis-based designing of oncogenic SHP2 peptide to inhibit cancer progression

Cancer is among the top causes of death, accounting for an estimated 9.6 million deaths in 2018, it appeared that approximately 500,000 people die from cancer in the United States alone annually. The SHP2 plays a major role in regulation of cell growth, proliferation, and differentiation, and functional upregulation of this enzyme is linked to oncogenesis and developmental disorders. SHP2 activity has been linked to several cancer types for which no drugs are currently available. In our study, we aimed to design peptide inhibitors against the SHP2 mutant. The crystal structure of the human Src SH2-PQpYEEIPI peptide mutant was downloaded from the protein databank. We generated several peptides from the native wild peptide using an in silico mutagenesis method, which showed that changes (P302W, Y304F, E306Q, and Q303A) might boost the peptide's affinity for binding to SHP2. Furthermore, the dynamical stability and binding affinities of the mutated peptide were confirmed using Molecular dynamics simulation and Molecular Mechanics with Generalized Born and Surface Area Solvation free energy calculations. The proposed substitution greatly enhanced the binding affinity at the residue level, according to a study that decomposed energy into its component residues. Our proposed peptide may prevent the spread of cancer by inhibiting SHP2, according to our detailed analyses of binding affinities.

Sunitinib selectively targets leukemogenic signaling of mutant SHP2 in juvenile myelomonocytic leukemia

Leukemogenic SHP2 mutations occur in 35% of patients with juvenile myelomonocytic leukemia (JMML), a hematopoietic malignancy with poor response to cytotoxic chemotherapy. Novel therapeutic strategies are urgently needed for patients with JMML. Previously, we established a novel cell model of JMML with HCD-57, a murine erythroleukemia cell line that depends on EPO for survival. SHP2-D61Y or -E76K drove the survival and proliferation of HCD-57 in absence of EPO. In this study, we identified sunitinib as a potent compound to inhibit SHP2-mutant cells by screening a kinase inhibitor library with our model. We used cell viability assay, colony formation assay, flow cytometry, immunoblotting, and a xenograft model to evaluate the effect of sunitinib against SHP2-mutant leukemia cells in vitro and in vivo. The treatment of sunitinib selectively induced apoptosis and cell cycle arrest in mutant SHP2-transformed HCD-57, but not parental cells. It also inhibited cell viability and colony formation of primary JMML cells with mutant SHP2, but not bone marrow mononuclear cells from healthy donors. Immunoblotting showed that the treatment of sunitinib blocked the aberrantly activated signals of mutant SHP2 with deceased phosphorylation levels of SHP2, ERK, and AKT. Furthermore, sunitinib effectively reduced tumor burdens of immune-deficient mice engrafted with mutant-SHP2 transformed HCD-57. Our data demonstrated that sunitinib selectively inhibited SHP2-mutant leukemia cells, which could serve as an effective therapeutic strategy for SHP2-mutant JMML in the future.

Abstract 873: The mechanisms of SHP2 activation in cancer and neurodevelopmental disorder

Abstract The Src homology 2 domain-containing phosphatase 2 (SHP2) is a nonreceptor protein tyrosine phosphatase that regulates Ras/MAPK pathway, leading to cell proliferation. SHP2 mutations are commonly associated with human malignancies and neurodevelopmental disorders (NDDs). Somatic SHP2 mutations are associated with many types of cancer including sporadic juvenile myelomonocytic leukemia, acute myeloid leukemia, breast, gastric, lung, melanoma, and colorectal cancers, while heterozygous germline mutations are linked to NDDs such as Noonan and LEOPARD syndromes. Interestingly, different mutations at the same genomic loci of the gene result in different disease phenotypes, either cancer or NDDs. Patients with NDDs have a higher chance of developing cancer, suggesting a linkage between cancer and NDDs, and between their mutations. SHP2 consists of two SH2 domains (nSH2 and cSH2), a phosphatase (PTP) domain, and a flexible C-terminal tail. In autoinhibition, SHP2 is catalytically inactive, adopting a closed conformation in which the DE-loop of nSH2 blocks the catalytic site of PTP. The binding of nSH2 to the phosphotyrosine (pY)-motif relieve the autoinhibition via disruption of the nSH2-PTP interface. To depict mechanism of the mutation-associated activation of SHP2, extensive molecular dynamics simulations were performed for SHP2 protein with the mutations related to cancer and NDDs. The dynamics and conformational alterations of the wild type, cancer mutants (E76K, D61Y, D61V), and NDD mutants (E76D, D61G) of SHP2 were compared. Collective results showed that both cancer and NDD mutations weaken the nSH2-PTP interface, facilitating the SHP2 activation. Interestingly, cancer mutations induce stronger destruction at the nSH2-PTP interface than the NDD mutations. The PTP domain exhibits two pockets, orthosteric and allosteric pockets, at the interface with nSH2. In autoinhibition, the orthosteric pocket provides a binding site for D61 of nSH2, and the allosteric pocket accommodates E76 and A72 of nSH2. During the simulations, we observed that the mutations, E76K and E76D, reduce the interaction in the allosteric pocket, increasing the probability toward the open SHP2 conformation. This gradually weakens the interactions of D61 in the orthosteric pocket, promoting SH2 release and leading to SHP2 activation. The three mutations, D61Y, D61V, and D61G, directly disrupted the interaction in the orthosteric pocket, favoring the substrate binding. However, they do not optimize the nSH2 conformation for the pY binding and unlikely affect the interaction in the allosteric pocket. Our works explain the difference and similarity between the cancer and NDD mutations of SHP2 at the atomic level and provide deeper understanding of the mutation-induced activation of SHP2 for signal transduction through the Ras/MAPK pathway. Citation Format: Yonglan Liu, Mingzhen Zhang, Wengang Zhang, Hyunbum Jang, Ruth Nussinov. The mechanisms of SHP2 activation in cancer and neurodevelopmental disorder [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 873.

THE FEATURES AND ROLE OF SHP2 PROTEIN IN POSTNATAL MUSCLE DEVELOPMENT

SHP-2 (encoded by PTPN11) is a ubiquitously expressed protein tyrosine phosphatase required for signal transduction by multiple different cell surface receptors. Humans with carry germline SHP-2 mutations develop Noonan syndrome or LEOPARD syndrome, which are characterized by cardiovascular, neurological and skeletal abnormalities.Shp2 is an important signaling agent for growth factors and cytokines. To investigate the Ptpn11 in postnatal myogenesis of mice  we analyzed using immunohistochemistry stem cell markers: Pax 7, Myo D, Myf 5 and Myo G in muscle cells isolated from wild type and Shp2 knockout mice. We used a conditional SHP-2 mouse mutant in which loss of expression of SHP-2 was induced in multiple tissues in response to drug administration. Our findings indicate that all these markers gradually decreased from birth to day 14 in mouse muscle cells. Here we show that Shp2, an intracellular tyrosine phosphatase with two SH2 domains, plays a critical role in mouse muscle development after birth. Our data demonstrate a molecular difference in the control and Sh2 knockout  postnatal myogenic stem cells, and assign to Ptpn11 signaling a key function in satellite cell activity. These findings illustrate an essential role for Shp-2 in muscle growth and remodeling in adults, and reveal some of the cellular and molecular mechanisms involved. The model is predicted to be of further use in understanding how Shp-2 regulates muscle morphogenesis, which could lead to the development of novel therapies for the treatment of malformations in human patients with SHP-2 mutations.

Transcriptome analysis reveals effects of leukemogenic SHP2 mutations in biosynthesis of amino acids signaling.

Gain-of-function mutations of SHP2, especially D61Y and E76K, lead to the development of neoplasms in hematopoietic cells. Previously, we found that SHP2-D61Y and -E76K confer HCD-57 cells cytokine-independent survival and proliferation via activation of MAPK pathway. Metabolic reprogramming is likely to be involved in leukemogenesis led by mutant SHP2. However, detailed pathways or key genes of altered metabolisms are unknown in leukemia cells expressing mutant SHP2. In this study, we performed transcriptome analysis to identify dysregulated metabolic pathways and key genes using HCD-57 transformed by mutant SHP2. A total of 2443 and 2273 significant differentially expressed genes (DEGs) were identified in HCD-57 expressing SHP2-D61Y and -E76K compared with parental cells as the control, respectively. Gene ontology (GO) and Reactome enrichment analysis showed that a large proportion of DEGs were involved in the metabolism process. Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis showed that DEGs were the mostly enriched in glutathione metabolism and biosynthesis of amino acids in metabolic pathways. Gene Set Enrichment Analysis (GSEA) revealed that the expression of mutant SHP2 led to a significant activation of biosynthesis of amino acids pathway in HCD-57 expressing mutant SHP2 compared with the control. Particularly, we found that ASNS, PHGDH, PSAT1, and SHMT2 involved in the biosynthesis of asparagine, serine, and glycine were remarkably up-regulated. Together, these transcriptome profiling data provided new insights into the metabolic mechanisms underlying mutant SHP2-driven leukemogenesis.

The Cell-Specific Role of SHP2 in Regulating Bone Homeostasis and Regeneration Niches.

Src homology-2 containing protein tyrosine phosphatase (SHP2), encoded by PTPN11, has been proven to participate in bone-related diseases, such as Noonan syndrome (NS), metachondromatosis and osteoarthritis. However, the mechanisms of SHP2 in bone remodeling and homeostasis maintenance are complex and undemonstrated. The abnormal expression of SHP2 can influence the differentiation and maturation of osteoblasts, osteoclasts and chondrocytes. Meanwhile, SHP2 mutations can act on the immune system, vasculature and nervous system, which in turn affect bone development and remodeling. Signaling pathways regulated by SHP2, such as mitogen-activated protein kinase (MAPK), Indian hedgehog (IHH) and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/protein kinase B (AKT), are also involved in the proliferation, differentiation and migration of bone functioning cells. This review summarizes the recent advances of SHP2 on osteogenesis-related cells and niche cells in the bone marrow microenvironment. The phenotypic features of SHP2 conditional knockout mice and underlying mechanisms are discussed. The prospective applications of the current agonists or inhibitors that target SHP2 in bone-related diseases are also described. Full clarification of the role of SHP2 in bone remodeling will shed new light on potential treatment for bone related diseases.

Aurora Kinase B/C Inhibitor GSK1070916 Specifically Targets Juvenile Myelomonocytic Leukemia Cells with SHP2(PTPN11) Mutation

Juvenile myelomonocytic leukemia (JMML) is a rare and fatal early childhood hematological malignancy. Somatic SHP2 mutation accounts for 30-40% of JMML, with poor prognosis and lack of effective therapy methods. Aurora kinases play important roles in chromosome alignment, segregation and cell division during mitosis. Malignant hematopoietic cell diseases, including acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), as well as chronic myeloid leukemia (CML), aberrantly express Aurora kinase A or B, which predict a poor overall prognosis. Aurora kinase represents a promising therapeutic target. However, to date there is no study on the relationship of aurora kinase and SHP2 mutant JMML. HCD57 cells are murine erythroleukemia cells that solely depend on exogenic erythropoietin (EPO) for survival. We constructed SHP2/D61Y and SHP2/E76K transformed HCD57 cells through retroviral transfection and selection. The two generated transformed cell lines (HCD57-SHP2/D61Y, HCD57-SHP2/E76K) were dependent on mutated-SHP2-mediated signaling. Based on these three cell lines, we screened 12 inhibitors, including aurora kinase A inhibitors, aurora kinase B inhibitors and pan-aurora kinase inhibitors. The selectivity and efficacy of the lead drugs were further evaluated on SHP2 mutant HCD57 cells and patient-derived PBMC cells by cell viability, flow cytometry, shRNA mediated gene silencing, western blotting and colony formation assays. Previous studies have shown that our established SHP2-mutant HCD57 cell line is a leukemia cell line representing the molecular signature of signaling pathways in SHP2 mutant JMML. The Aurora kinase B/C inhibitor GSK1070916 selectively inhibited SHP2-mutant HCD57 cells through drug screening. Cell viability assay demonstrated a dose-dependent inhibition pattern of HCD57-SHP2/D61Y and HCD57-SHP2/E76K cells and had no significant inhibition effect on parental HCD57 cells. GSK1070916 induced cell cycle arrest at G2/M phase and cell apoptosis in HCD57-SHP2/D61Y and HCD57-SHP2/E76K cells. Although HCD57 cells were also arrested in G2/M phase after GSK1070916C treatment, the cells did not show significant apoptosis. Western blot analysis showed that the protein level of anti-apoptotic protein Bcl-xL demonstrated a time-dependent increase, while caspase-3 and PARP proteins had no obvious cleavage in HCD57 cells after treatment of GSK1070916. However, in HCD57-SHP2/D61Y and HCD57-SHP2/E76K cells, protein level of Bcl-xL was not significantly increased, while the cleaved form of caspase-3 and PARP significantly increased. This result demonstrated that SHP2-mutant cells were less capable in generating pro-survival signal and was sensitive to the inhibition of AURKB. Furthermore, the phenotype induced through silencing Aurkb by shRNA was similar to the inhibition effect of GSK1070916. We further investigated the ex vivo inhibitory effect of GSK1070916 on JMML patient-derived PBMC cells (mutation type: SHP2/E76A). The colony-forming ability of primary JMML cells was completely inhibited under treatment of GSK1070916 (500 nM). In conclusion, aurora kinase B can be used as a promising therapeutic target for SHP2-mutant JMML patients, and the aurora kinase B/C inhibitor GSK1070916 could be a candidate for the treatment of JMML.

SHP-2 Regulates Myeloid Cell Differentiation, Anti-Tumor Responses and Innate Immune Memory

PD-1 is a T cell checkpoint inhibitor and the most extensively exploited therapeutic target of cancer immunotherapy. PD-1-mediated T cell inactivation is attributed to the function of SHP-2 phosphatase, which is activated by recruitment to PD-1 cytoplasmic tail. However, T cell-specific SHP-2 deletion did not improve anti-tumor immunity or altered responses to anti-PD-1 immunotherapy. Previously, we determined that PD-1 is also expressed in common myeloid progenitors and granulocyte/macrophage progenitors, which accumulate during cancer-driven emergency myelopoiesis and give rise to immunosuppressive myeloid-derived suppressor cells (MDSC) and tumor-associated macrophages (TAMs). In tumor-bearing mice with myeloid-specific PD-1 ablation, accumulation of MDSCs was prevented, while output of differentiated effector myeloid cells with monocytic lineage dominance was increased. However, the molecular mechanism remains elusive. It is also unknown whether a canonical PD-1:SHP-2 axis is operative in myeloid cells. Temporal activation of SHP-2 is critical for myeloid cell fate. Gain of function SHP-2 mutations, resulting in constitutive phosphatase activation, prevent myeloid differentiation and lead to the accumulation of immature myelocytes and development of leukemia. HOXA proteins, members of the HOX family of transcription factors involved in normal hematopoiesis, are targets of SHP-2, which dephosphorylates HOXA and prevents derepressing of HOXA target genes and myeloid cell differentiation. In addition, SHP-2 regulates the function of IFN regulatory factor (IRF)-8, a transcription factor that has a decisive role in myeloid progenitor differentiation toward monocytes and DCs. IRF8 phosphorylation is mandatory for its nuclear translocation and initiation of gene transcription. The cytoplasmic-nuclear shuttling of IRF8 is regulated by SHP-2, which dephosphorylates IRF8 and prevents its nuclear localization and transcriptional activation. We generated mice with conditional targeting of the Ptpn11 gene (encoding for Shp-2) in T cells (Shp2f/fLckCre) or myeloid cells (Shp2f/fLysMCre), and found that Shp2f/fLysMCre but not Shp2f/fLckCre mice had diminished tumor growth. As determined by RNA-sequencing, this was paralleled by the presence of inflammatory neutrophils and tumor-associated macrophages (TAMs) with molecular signatures of enhanced differentiation, phagocytosis and antigen-processing and presentation. SHP-2 deficient TAMs also had increased monocyte and dendritic cells (DCs) specification transcription factors, chemokine and cytokine production, and expression of immunostimulatory molecules that promote T cell recruitment and activation. Moreover, monocytes from tumor-bearing Shp2f/fLysMCre mice suppressed tumor growth after transfer to naïve recipients indicating development of innate immune memory, named trained immunity. In bone marrow myelocytes, SHP-2 deletion enhanced GM-CSF-mediated phosphorylation of the transcription factors HOXA10 and IRF8 that promote myeloid differentiation and monocytic/moDC lineage commitment, respectively. In contrast, in WT bone marrow myelocytes GM-CSF induced PD-1 expression, phosphorylation and interaction with SHP-2, the Src family kinase Lyn, and GM-CSF receptor beta chain, indicating that the PD-1:SHP-2 axis targets a key pathway of myelocyte differentiation. Our results reveal a previously unidentified mechanistic role of SHP-2 and the PD-1:SHP-2 axis in regulating myeloid cell differentiation in the context of cancer and provide evidence that SHP-2 poses a signaling restrain to myeloid differentiation and monocyte lineage commitment resulting in a myeloid landscape that suppresses anti-tumor immunity. This process is hijacked by the PD-1/PD-L1 pathway.