Pyrophosphatase overexpression is associated with cell migration, invasion, and poor prognosis in gastric cancer

Identification of PPA1 inhibitor candidates for potential repurposing in cancer medicine

Inorganic pyrophosphatase 1 (PPA1) is pivotal to cellular metabolism as it facilitates the hydrolysis of PPi-a by-product of various metabolic processes that influence cell growth and differentiation. Overexpression of PPA1 enzyme has been linked to diminished patient survival and was shown to influence tumor cell dynamics, thereby positioning it as a potential therapy target for a variety of cancers including colorectal cancer, diffuse large B-cell lymphoma, and lung adenocarcinoma. Despite this therapeutic promise, there are no known inhibitors of PPA1 as of today. In this study, we searched for potential PPA1 inhibitors using a molecular docking screen of 30 470 compounds with a history of clinical trials and/or US Food and Drug Administration approval. We specifically targeted the active pocket that coincides with the established catalytic domain. Our screen identified promising hits, which we further subjected to ADMET (absorption, distribution, metabolism, excretion, and toxicity) filtering. Subsequent molecular dynamics (MD) analyses were conducted on devazepide, quinotolast, and tarazepide-the three substances that successfully navigated all filters. MD analyses reinforced the stability of the protein-ligand complexes and confirmed ligand binding, as substantiated by our root mean square deviation, radius of gyration and secondary structures of proteins analyses. Furthermore, Molecular Mechanics Poisson-Boltzmann Surface Area calculations post-MD identified devazepide and quinotolast as showing higher binding affinities; being supported by principal component analysis, free energy landscape, and dynamic cross-correlation matrix results. Overall, our study reveals devazepide and quinotolast as potential candidates for PPA1 inhibition which could be considered for repurposing studies that need further experimental validation. These results not only reveal a potential for clinical repurposing for PPA1 inhibition but they also offer valuable insights into the development of future compounds for targeting the crucial PPA1 enzyme.

PPA1, an energy metabolism initiator, plays an important role in the progression of malignant tumors

Inorganic pyrophosphatase (PPA1) encoded by PPA1 gene belongs to Soluble Pyrophosphatases (PPase) family and is expressed widely in various tissues of Homo sapiens, as well as significantly in a variety of malignancies. The hydrolysis of inorganic pyrophosphate (PPi) to produce orthophosphate (Pi) not only dissipates the negative effects of PPi accumulation, but the energy released by this process also serves as a substitute for ATP. PPA1 is highly expressed in a variety of tumors and is involved in proliferation, invasion, and metastasis during tumor development, through the JNK/p53, Wnt/β-catenin, and PI3K/AKT/GSK-3β signaling pathways. Because of its remarkable role in tumor development, PPA1 may serve as a biological target for adjuvant therapy of tumor malignancies. Further, PPA1 is a potential biomarker to predict survival in patients with cancer, where the assessment of its transcriptional regulation can provide an in-depth understanding. Herein, we describe the signaling pathways through which PPA1 regulates malignant tumor progression and provide new insights to establish PPA1 as a biomarker for tumor diagnosis.

Crystallographic and modeling study of the human inorganic pyrophosphatase 1: A potential anti-cancer drug target

Inorganic pyrophosphatases (PPases) catalyze the hydrolysis of pyrophosphate to phosphates. PPases play essential roles in growth and development, and are found in all kingdoms of life. Human possess two PPases, PPA1 and PPA2. PPA1 is present in all tissues, acting largely as a housekeeping enzyme. Besides pyrophosphate hydrolysis, PPA1 can also directly dephosphorylate phosphorylated c-Jun N-terminal kinases 1 (JNK1). Upregulated expression of PPA1 has been linked to many human malignant tumors. PPA1 knockdown induces apoptosis and decreases proliferation. PPA1 is emerging as a potential prognostic biomarker and target for anti-cancer drug development. In spite of the biological and physiopathological importance of PPA1, there is no detailed study on the structure and catalytic mechanisms of mammalian origin PPases. Here we report the crystal structure of human PPA1 at a resolution of 2.4 Å. We also carried out modeling studies of PPA1 in complex with JNK1 derived phosphor-peptides. The monomeric protein fold of PPA1 is similar to those found in other family I PPases. PPA1 forms a dimeric structure that should be conserved in animal and fungal PPases. Analysis of the PPA1 structure and comparison with available structures of PPases from lower organisms suggest that PPA1 has a largely pre-organized and relatively rigid active site for pyrophosphate hydrolysis. Results from the modeling study indicate the active site of PPA1 has the potential to accommodate double-phosphorylated peptides from JNK1. In short, results from the study provides new insights into the mechanisms of human PPA1 and basis for structure-based anti-cancer drug developments using PPA1 as the target.

Pyrophosphatase 1 expression is associated with future recurrence and overall survival in Chinese patients with intrahepatic cholangiocarcinoma

The inorganic pyrophosphatase gene (PPA1) encodes inorganic pyrophosphatase, an enzyme that catalyzes the hydrolysis of inorganic pyrophosphate to orthophosphate, and has been revealed to be dysregulated in several types of human cancer. However, the role of PPA1 in intrahepatic cholangiocarcinoma (ICC) has not yet been determined. The present study detected PPA1 expression and investigated its clinical significance in ICC. Tissue microarray blocks containing 93 ICC specimens were constructed. The protein expression of PPA1 in these specimens was detected by immunohistochemistry. PPA1 was overexpressed in 49.5% of the ICC specimens and was significantly associated with large tumor size, positive margins, T stage, lymph nodal metastases, poorly differentiated tumors and advanced disease stage. Furthermore, PPA1 expression was an indicator of future recurrence and poor survival in patients with ICC. Increased expression of PPA1 is a common event in human ICC and is significantly associated with a poor outcome in patients with ICC, suggesting a potential role for PPA1 in the development and progression of ICC.

Clinical significance and functional validation of inorganic pyrophosphatase in diffuse large B cell lymphoma in humans

Diffuse large B-cell lymphoma (DLBCL), the most common type of non-Hodgkin's lymphoma, displays marked heterogeneity. Although it is usually curable, 30-40% of patients die within 1-2 years due to refractory treatment or cancer relapse. In different types of cancer in humans, inorganic pyrophosphatase (PPA1) is deregulated, thereby contributing to tumorigenesis by supplying the tumor with an enormous energy source. However, the role of PPA1 in DLBCL is still unclear. Here, we analized PPA1 in 65 patients with DLBCL and 20 patients with reactive hyperplasia of the lymph nodes (control). The PPA1 level was significantly higher in patients with DLBCL than in control subjects (p < 0.05), and it is closely associated with B symptoms (i.e., fever, night sweats, and weight loss) and the IPI score (p < 0.05). Furthermore, PPA1 mRNA and protein levels were higher in most DLBCL cell lines than in the control HMy2.CIR cell line. Lastly, we investigated the effects of PPA1 knockdown on the proliferation and survival of the DLBCL cell line. We found that p53 and p21 expression decreased in PPA1-silenced DLBCL cells. In addition, cell proliferation decreased and cell apoptosis increased. In conclusion, PPA1 is a novel molecule that may be useful in the development and prognosis of DLBCL in the future.

Silencing PPA1 inhibits human epithelial ovarian cancer metastasis by suppressing the Wnt/β-catenin signaling pathway

Inorganic pyrophosphatase (PPA1) activity is a key determinant of cellular inorganic pyrophosphate levels, and its expression is correlated with growth of several solid tumors. To investigate this relationship, we first examined PPA1 expression in human epithelial ovarian cancer (EOC) samples, and found that PPA1 was overexpressed in tumors from EOC patients. Higher PPA1 levels correlated with advanced grades, stages, and poor survival in EOC patients. Examination of PPA1 function in EOC revealed that silencing PPA1 inhibited EOC migration, epithelial-mesenchymal transition (EMT), and metastasis in vitro and in vivo. In addition, PPA1 may promote the dephosphorylation and translocation of β-catenin. These results demonstrate that silencing PPA1 inhibits EOC metastasis by suppressing the Wnt/β-catenin signaling pathway. Strategies for downregulating PPA1 may have therapeutic potential for the prevention and treatment of EOC.

WWC3 downregulation correlates with poor prognosis and inhibition of Hippo signaling in human gastric cancer

The aim of this study was to investigate the clinicopathological significance and biological roles of WWC3 in human gastric cancer (GC). Clinical significance of WWC3 in human GCs was examined by using immunohistochemistry (IHC). WWC3 was downregulated in 48 of 111 human GCs, and its downregulation was associated with advanced stage, positive nodal status, and higher relapse rate. Importantly, WWC3 downregulation correlated with poor survival. It was also found that WWC3 protein expression was downregulated in GC cell lines compared with normal cell line GES-1. On one hand, WWC3 overexpression inhibited the cell growth rate and invading ability in HGC-27 cell line. On the other hand, depleting WWC3 by small interfering RNA (siRNA) promoted proliferation rate and invading ability in the SGC-7901 cell line. In addition, cell cycle analysis showed that WWC3 overexpression inhibited while its depletion accelerated cell cycle progression at the G1/S transition. Western blot (WB) analysis demonstrated that WWC3 repressed cyclin D1 and cyclin E while upregulated p27 expression. Luciferase reporter assay showed that WWC3 activated Hippo signaling pathway by suppressing TEAD transcription activity, with downregulation of total and nuclear YAP and its target CTGF. WWC3 siRNA depletion exhibited the opposite effects. In conclusion, this study indicates that WWC3 serves as a tumor suppressor in GC by activating Hippo signaling.

Prediction of adjuvant chemotherapy response in triple negative breast cancer with discovery and targeted proteomics

BACKGROUND

Triple-negative breast cancer (TNBC) accounts for 15-20% of all breast cancers and usually requires the administration of adjuvant chemotherapy after surgery but even with this treatment many patients still suffer from a relapse. The main objective of this study was to identify proteomics-based biomarkers that predict the response to standard adjuvant chemotherapy, so that patients at are not going to benefit from it can be offered therapeutic alternatives.

METHODS

We analyzed the proteome of a retrospective series of formalin-fixed, paraffin-embedded TNBC tissue applying high-throughput label-free quantitative proteomics. We identified several protein signatures with predictive value, which were validated with quantitative targeted proteomics in an independent cohort of patients and further evaluated in publicly available transcriptomics data.

RESULTS

Using univariate Cox analysis, a panel of 18 proteins was significantly associated with distant metastasis-free survival of patients (p<0.01). A reduced 5-protein profile with prognostic value was identified and its prediction performance was assessed in an independent targeted proteomics experiment and a publicly available transcriptomics dataset. Predictor P5 including peptides from proteins RAC2, RAB6A, BIEA and IPYR was the best performance protein combination in predicting relapse after adjuvant chemotherapy in TNBC patients.

CONCLUSIONS

This study identified a protein combination signature that complements histopathological prognostic factors in TNBC treated with adjuvant chemotherapy. The protein signature can be used in paraffin-embedded samples, and after a prospective validation in independent series, it could be used as predictive clinical test in order to recommend participation in clinical trials or a more exhaustive follow-up.

PPA1 regulates tumor malignant potential and clinical outcome of colon adenocarcinoma through JNK pathways

Colorectal cancer (CRC) represents one of the most prevalent malignancies and the third leading cause of cancer death worldwide. Inorganic pyrophosphatase (PPA1) is an enzyme that catalyzes the hydrolysis of pyrophosphate to inorganic phosphate, therefore participates in the energy metabolism. Proteomic studies have demonstrated the up-regulated expression of PPA1 in various tumors, however, its expression pattern in CRC hasn't been reported. In the current study, we used RT-qCR, Western Blot and immunohistochemical (IHC) staining to explore the expression of PPA1 in 113 paired colon cancer tissues and adjacent normal tissues, which revealed that PPA1 was correlated with lymph node metastasis. The prognostic value of PPA1 was confirmed by Kaplan-Meier survival analysis and Cox regression analysis. We further purified PPA1 and obtained the phosphor-JNK1 protein and performed enzymatic studies, which identified that PPA1 can directly dephosphorylate pJNK1, while showed no catalytic activity towards pERK or p-p38 proteins. Moreover, overexpression of PPA1 enhanced cell viability through JNK-p53 signaling pathways, and it may also prevent cell apoptosis by inhibiting Bcl-2 and Caspase-3 cleavage. To our knowledge, this is the first study demonstrated the expression and clinical significance of PPA1 in colon cancer, which also provided evidence that figuring out PPA1 specific inhibitors can be invaluable in the future chemotherapy development towards colon cancer.

Tbx3 overexpression in human gastric cancer is correlated with advanced tumor stage and nodal status and promotes cancer cell growth and invasion

The objective of the current study was to investigate the expression pattern of Tbx3 and its clinicopathological significance in patients with gastric cancer. The expression pattern of Tbx3 in gastric cancer tissues and adjacent noncancerous surface epithelia and mucosal glands was detected by immunohistochemistry. Tbx3 was found to be overexpressed in 46 of 98 human gastric cancer samples, and this correlated with advanced clinical stage, tumor stage, and nodal status. In addition, in the SGC-7901 gastric cancer cell line, Tbx3 overexpression by plasmid transfection promoted growth and invasion. Conversely, depleting Tbx3 expression by small-interfering RNA inhibited proliferation and invasion in BGC-823 cell line. Moreover, Tbx3 accelerated cell cycle progression at the G1/S boundary. Tbx3 also regulated epithelial-to-mesenchymal transition (EMT) to promote cell invasion by repressing E-cadherin expression and increasing expression levels N-cadherin, vimentin. These results indicate that in gastric cancer, Tbx3 plays an important role and might be a useful therapy target.

Identification of Critical Elements for Regulation of Inorganic Pyrophosphatase (PPA1) in MCF7 Breast Cancer Cells

Cytosolic inorganic pyrophosphatase plays an important role in the cellular metabolism by hydrolyzing inorganic pyrophosphate (PPi) formed as a by-product of various metabolic reactions. Inorganic pyrophosphatases are known to be associated with important functions related to the growth and development of various organisms. In humans, the expression of inorganic pyrophosphatase (PPA1) is deregulated in different types of cancer and is involved in the migration and invasion of gastric cancer cells and proliferation of ovarian cancer cells. However, the transcriptional regulation of the gene encoding PPA1 is poorly understood. To gain insights into PPA1 gene regulation, a 1217 bp of its 5'-flanking region was cloned and analyzed. The 5'-deletion analysis of the promoter revealed a 266 bp proximal promoter region exhibit most of the transcriptional activity and upon sequence analysis, three putative Sp1 binding sites were found to be present in this region. Binding of Sp1 to the PPA1 promoter was confirmed by Electrophoretic mobility shift assay (EMSA) and Chromatin immunoprecipitation (ChIP) assay. Importance of these binding sites was verified by site-directed mutagenesis and overexpression of Sp1 transactivates PPA1 promoter activity, upregulates protein expression and increases chromatin accessibility. p300 binds to the PPA1 promoter and stimulates Sp1 induced promoter activity. Trichostatin A (TSA), a histone deacetylase (HDAC) inhibitor induces PPA1 promoter activity and protein expression and HAT activity of p300 was important in regulation of PPA1 expression. These results demonstrated that PPA1 is positively regulated by Sp1 and p300 coactivates Sp1 induced PPA1 promoter activity and histone acetylation/deacetylation may contribute to a local chromatin remodeling across the PPA1 promoter. Further, knockdown of PPA1 decreased colony formation and viability of MCF7 cells.

TRIM24 is upregulated in human gastric cancer and promotes gastric cancer cell growth and chemoresistance

The tripartite motif protein tripartite motif-containing 24 (TRIM24) is involved in human cancer progression. However, the expression pattern and biological roles of TRIM24 in human gastric cancer have not been studied. Here, we report that expression of TRIM24 protein was upregulated in 65 of 133 gastric cancer specimens. TRIM24 upregulation positively correlated with clinical stage, local invasion, and poor patient prognosis. We overexpressed TRIM24 by transfection in SGC-7901 cells and used an siRNA strategy to knock down TRIM24 in MKN-1 cells. MTT and colony formation assays showed that transfection of TRIM24 plasmid accelerated, while its depletion inhibited cell proliferation rate. TRIM24 overxpression also induced chemoresistance to 5-FU in gastric cancer cells. Further analysis showed that TRIM24 overexpression upregulated cyclin D1 and Akt phosphorylation. Akt inhibitor LY294002 reversed the role of TRIM24 on chemoresistance. In conclusion, our study shows that TRIM24 is overexpressed in human gastric cancer and accelerates cell growth as well as induce chemoresistance, possibly through the Akt pathway.

Understanding protein-nanoparticle interaction: a new gateway to disease therapeutics

Molecular identification of protein molecules surrounding nanoparticles (NPs) may provide useful information that influences NP clearance, biodistribution, and toxicity. Hence, nanoproteomics provides specific information about the environment that NPs interact with and can therefore report on the changes in protein distribution that occurs during tumorigenesis. Therefore, we hypothesized that characterization and identification of protein molecules that interact with 20 nm AuNPs from cancer and noncancer cells may provide mechanistic insights into the biology of tumor growth and metastasis and identify new therapeutic targets in ovarian cancer. Hence, in the present study, we systematically examined the interaction of the protein molecules with 20 nm AuNPs from cancer and noncancerous cell lysates. Time-resolved proteomic profiles of NP-protein complexes demonstrated electrostatic interaction to be the governing factor in the initial time-points which are dominated by further stabilization interaction at longer time-points as determined by ultraviolet-visible spectroscopy (UV-vis), dynamic light scattering (DLS), ζ-potential measurements, transmission electron microscopy (TEM), and tandem mass spectrometry (MS/MS). Reduction in size, charge, and number of bound proteins were observed as the protein-NP complex stabilized over time. Interestingly, proteins related to mRNA processing were overwhelmingly represented on the NP-protein complex at all times. More importantly, comparative proteomic analyses revealed enrichment of a number of cancer-specific proteins on the AuNP surface. Network analyses of these proteins highlighted important hub nodes that could potentially be targeted for maximal therapeutic advantage in the treatment of ovarian cancer. The importance of this methodology and the biological significance of the network proteins were validated by a functional study of three hubs that exhibited variable connectivity, namely, PPA1, SMNDC1, and PI15. Western blot analysis revealed overexpression of these proteins in ovarian cancer cells when compared to normal cells. Silencing of PPA1, SMNDC1, and PI15 by the siRNA approach significantly inhibited proliferation of ovarian cancer cells and the effect correlated with the connectivity pattern obtained from our network analyses.

PBX3 is overexpressed in gastric cancer and regulates cell proliferation

The pre-leukemia transcription factor 3 (PBX3) is a member of the PBX family of transcription factors, which is known to increase DNA-binding/transcriptional activity of HOX proteins and regulate genes involved in development. Recently, PBX3 was reported to be involved in a variety of cancers, while its implication in gastric cancer is unclear. This study aimed to investigate its clinical significance and biological function in gastric cancer. PBX3 expression was analyzed in 90 gastric cancer specimens using immunohistochemistry. PBX3 was overexpressed in 30 cases (33.33%). Importantly, PBX3 overexpression positively correlated with advanced invasion depth (p = 0.0017), Clinical stage (p = 0.0127) and grade of tumor differentiation (p = 0.0158). PBX3 was also overexpressed in gastric cancer cell lines. Plasmid transfection was performed in AGS and SGC-7901 gastric cancer cell line with low endogenous PBX3 expression. MTT and colony formation assay were carried out to assess the role of PBX3 in proliferation. PBX3 overexpression in gastric cancer cell lines accelerated cell proliferation rate and colony formation ability, with upregulation of PCNA expression. In addition, matrigel invasion assay showed that PBX3 transfection also increased cell-invading ability. These results validate the role of PBX3 as a clinically relevant oncoprotein and establish PBX3 as a promising therapeutic target of gastric cancer.

Age-dependent increased expression and activity of inorganic pyrophosphatase in the liver of male mice and its further enhancement with short- and long-term dietary restriction

Intracellular orthophosphate and inorganic pyrophosphate (PPi) are by-products of multiple biosynthetic reactions. PPi hydrolysis by soluble inorganic pyrophosphatase (iPPase) has been considered as an important homeostatic mechanism. We investigated the expression and activities (U/mg protein) of iPPase in the liver of young and old mice subjected to short- and long-term dietary restriction. The expression level of iPPase was ascertained by the Western blot analysis using anti-iPPase and differential polymerase chain reaction using iPPase specific primer. Older mice showed a significant increase in the expression and activity of iPPase as compared to younger ones. Short-term fasting of 24 h increased the expression and activity of iPPase in the liver of both young and old mice which were reversed upon 24 h of re-feeding them. However, both young and old mice on long-term dietary restriction showed a cumulative increase in the expression and activity of iPPase when compared with their age-matched controls. This might be due to accumulative adaptation to refill energy deficiency of long-term dietary restricted mice for ATP generation via oxidative phosphorylation, where fatty acid activation could be driven by elevated iPPase.

dCTP pyrophosphohydrase exhibits nucleic accumulation in multiple carcinomas

Nucleoside triphosphate pyrophosphohydrolase (NTP-PPase) functions as one of the mechanisms to guarantee the fidelity of DNA replication through the cleavage of non-canonical nucleotides into di- or monophosphates. Human NTP-PPase is poorly understood and investigated. In the present study, by using tissue microarrays with the paired cancer and adjacent regions, we found that with the prevalent expression of dCTP pyrophosphohydrase (DCTPP1) in the cytosol and nucleus in tumors investigated, DCTPP1 was inclined to accumulate in the nucleus of cancer cells compared to the paired adjacent tissue cells in multiple carcinomas including lung, breast, liver, cervical, gastric and esophagus cancer. More significantly, the higher DCTPP1 expression in the nucleus of lung, gastric and esophagus cancer cells was associated with histological subtypes. The nucleic accumulation of DCTPP1 was apparently observed as well when tumor cell line MCF-7 was treated with H₂O₂in vitro. Considering the roles of DCTPP1 on restricting the concentration of non-canonical nucleotides in the nucleotide pool, accumulation of DCTPP1 in the nucleus of tumor cells might suffice for maintaining the proper DNA replication in order to fulfill the requirement for the survival and proliferation of tumor cells.

Glutathione S-transferase P1 Ile105Val polymorphism contributes to increased risk of gastric cancer in East Asians

Glutathione S-transferase P1 (GSTP1) is an important enzyme playing critical roles in the phase II detoxification pathway. There were many studies investigating the association between GSTP1 gene Ile105Val polymorphism and gastric cancer risk, but studies from East Asians reported inconsistent findings. We performed a meta-analysis to investigate the association in East Asians. Published literature from PubMed and Chinese Biomedical Literature databases were searched for eligible publications. Pooled odds ratios (ORs) with 95 % confidence intervals (95 %CIs) were calculated using random or fixed-effect model according the between-study heterogeneity. A total of 12 studies with 2,552 cases and 5,474 controls were finally included into the meta-analysis. Meta-analysis of those 12 studies showed that there was an obvious association between GSTP1 Ile105Val polymorphism and gastric cancer risk in East Asians under three genetic models (for valine vs. isoleucine, OR=1.32, 95 %CI 1.05-1.66, P=0.015; for ValVal vs. IleIle, OR=2.00, 95 %CI 1.34-2.98, P=0.001; for the recessive model, OR=1.96, 95 %CI 1.35-2.83, P<0.001). Sensitivity analysis by removing one study at a time suggested the pooled results were stable under the three genetic models above. There was no risk of publication bias. In conclusion, the meta-analysis suggests that there is a strong evidence for the association between GSTP1 Ile105Val polymorphism and increased risk of gastric cancer in East Asians and contributes to increased risk of gastric cancer in East Asians.