Targeted Quantitative Kinome Analysis Identifies PRPS2 as a Promoter for Colorectal Cancer Metastasis

Regulatory mechanism and expression level of PRPS2 in lung cancer

BACKGROUND

Lung cancer, with high morbidity and mortality, is the commonest respiratory system neoplasm, which seriously endangers the life safety of patients. In this study, the effect of PRPS2 on cell progression was preliminarily investigated.

METHODS

Immunohistochemical staining, western blot and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) were performed to verify the expression level of PRPS2 in lung cancer. Lung cancer cell lines with stable downregulation of PRPS2 were constructed in A549 cells and NCIH460 cells. The function of PRPS2 silencing on the proliferation ability was verified by the EdU and cell colony formation experiment. Scratch and transwell tests were conducted to verify the role of PRPS2 silencing on the migratory and invasive ability of cells. The impact of PRPS2 silencing on cell apoptosis and cell cycle was verified by flow cytometry test. The effects of PRPS2 silencing on apoptosis-associated proteins were assessed by western blot assay. The function of PRPS2 silencing on tumor growth in vivo was studied through xenograft tumor experiment.

RESULTS

In comparison with normal tissues, PRPS2 was upregulated in lung cancer tissues. PRPS2 knockdown notably hindered the migratory ability, invasive ability and proliferation, but accelerated cell apoptosis. In vivo experiments confirmed that PRPS2 silencing blocked the growth of transplanted tumors.

CONCLUSION

In lung cancer, PRPS2 silencing suppressed the malignant progression, indicating that PRPS2 might be a novel biomarker for lung cancer treatment and diagnosis.

The Proteome Profile of Olfactory Ecto-Mesenchymal Stem Cells-Derived from Patients with Familial Alzheimer's Disease Reveals New Insights for AD Study

Alzheimer's disease (AD), the most common neurodegenerative disease and the first cause of dementia worldwide, has no effective treatment, and its pathological mechanisms are not yet fully understood. We conducted this study to explore the proteomic differences associated with Familial Alzheimer's Disease (FAD) in olfactory ecto-mesenchymal stem cells (MSCs) derived from PSEN1 (A431E) mutation carriers compared with healthy donors paired by age and gender through two label-free liquid chromatography-mass spectrometry approaches. The first analysis compared carrier 1 (patient with symptoms, P1) and its control (healthy donor, C1), and the second compared carrier 2 (patient with pre-symptoms, P2) with its respective control cells (C2) to evaluate whether the protein alterations presented in the symptomatic carrier were also present in the pre-symptom stages. Finally, we analyzed the differentially expressed proteins (DEPs) for biological and functional enrichment. These proteins showed impaired expression in a stage-dependent manner and are involved in energy metabolism, vesicle transport, actin cytoskeleton, cell proliferation, and proteostasis pathways, in line with previous AD reports. Our study is the first to conduct a proteomic analysis of MSCs from the Jalisco FAD patients in two stages of the disease (symptomatic and presymptomatic), showing these cells as a new and excellent in vitro model for future AD studies.

On-demand utilization of phosphoribosyl pyrophosphate by downstream anabolic pathways

The pentose phosphate pathway (PPP) is critical for anabolism and biomass production. Here we show that the essential function of PPP in yeast is the synthesis of phosphoribosyl pyrophosphate (PRPP) catalyzed by PRPP-synthetase. Using combinations of yeast mutants, we found that a mildly decreased synthesis of PRPP affects biomass production, resulting in reduced cell size, while a more severe decrease ends up affecting yeast doubling time. We establish that it is PRPP itself that is limiting in invalid PRPP-synthetase mutants and that the resulting metabolic and growth defect can be bypassed by proper supplementation of the medium with ribose-containing precursors or by the expression of bacterial or human PRPP-synthetase. In addition, using documented pathologic human hyperactive forms of PRPP-synthetase, we show that intracellular PRPP as well as its derived products can be increased in both human and yeast cells, and we describe the ensuing metabolic and physiological consequences. Finally, we found that PRPP consumption appears to take place "on demand" by the various PRPP-utilizing pathways, as shown by blocking or increasing the flux in specific PRPP-consuming metabolic routes. Overall, our work reveals important similarities between human and yeast for both synthesis and consumption of PRPP.

Targeted Proteomic Approaches for Proteome-Wide Characterizations of the AMP-Binding Capacities of Kinases

Kinases play important roles in cell signaling, and adenosine monophosphate (AMP) is known to modulate cellular energy homeostasis through AMP-activated protein kinase (AMPK). Here, we explored novel AMP-binding kinases by employing a desthiobiotin-conjugated AMP acyl-phosphate probe to enrich efficiently AMP-binding proteins. Together with a parallel-reaction monitoring-based targeted proteomic approach, we uncovered 195 candidate AMP-binding kinases. We also enriched desthiobiotin-labeled peptides from adenine nucleotide-binding sites of kinases and analyzed them using LC-MS/MS in the multiple-reaction monitoring mode, which resulted in the identification of 44 peptides derived from 43 kinases displaying comparable or better binding affinities toward AMP relative to adenosine triphosphate (ATP). Moreover, our proteomic data revealed a potential involvement of AMP in the MAPK pathway through binding directly to the relevant kinases, especially MEK2 and MEK3. Together, we revealed the AMP-binding capacities of a large number of kinases, and our work built a strong foundation for understanding how AMP functions as a second messenger to modulate cell signaling.

Contribution of Model Organisms to Investigating the Far-Reaching Consequences of PRPP Metabolism on Human Health and Well-Being

Phosphoribosyl pyrophosphate synthetase (PRS EC 2.7.6.1) is a rate-limiting enzyme that irreversibly catalyzes the formation of phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate and adenosine triphosphate (ATP). This key metabolite is required for the synthesis of purine and pyrimidine nucleotides, the two aromatic amino acids histidine and tryptophan, the cofactors nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), all of which are essential for various life processes. Despite its ubiquity and essential nature across the plant and animal kingdoms, PRPP synthetase displays species-specific characteristics regarding the number of gene copies and architecture permitting interaction with other areas of cellular metabolism. The impact of mutated PRS genes in the model eukaryote Saccharomyces cerevisiae on cell signalling and metabolism may be relevant to the human neuropathies associated with PRPS mutations. Human PRPS1 and PRPS2 gene products are implicated in drug resistance associated with recurrent acute lymphoblastic leukaemia and progression of colorectal cancer and hepatocellular carcinoma. The investigation of PRPP metabolism in accepted model organisms, e.g., yeast and zebrafish, has the potential to reveal novel drug targets for treating at least some of the diseases, often characterized by overlapping symptoms, such as Arts syndrome and respiratory infections, and uncover the significance and relevance of human PRPS in disease diagnosis, management, and treatment.

Neuregulin (NRG-1β) Is Pro-Myogenic and Anti-Cachectic in Respiratory Muscles of Post-Myocardial Infarcted Swine

Neuregulin-1β (NRG-1β) is a growth and differentiation factor with pleiotropic systemic effects. Because NRG-1β has therapeutic potential for heart failure and has known growth effects in skeletal muscle, we hypothesized that it might affect heart failure-associated cachexia, a severe co-morbidity characterized by a loss of muscle mass. We therefore assessed NRG-1β's effect on intercostal skeletal muscle gene expression in a swine model of heart failure using recombinant glial growth factor 2 (USAN-cimaglermin alfa), a version of NRG-1β that has been tested in humans with systolic heart failure. Animals received one of two intravenous doses (0.67 or 2 mg/kg) of NRG-1β bi-weekly for 4 weeks, beginning one week after infarct. Based on paired-end RNA sequencing, NRG-1β treatment altered the intercostal muscle gene expression of 581 transcripts, including genes required for myofiber growth, maintenance and survival, such as MYH3, MYHC, MYL6B, KY and HES1. Importantly, NRG-1β altered the directionality of at least 85 genes associated with cachexia, including myostatin, which negatively regulates myoblast differentiation by down-regulating MyoD expression. Consistent with this, MyoD was increased in NRG-1β-treated animals. In vitro experiments with myoblast cell lines confirmed that NRG-1β induces ERBB-dependent differentiation. These findings suggest a NRG-1β-mediated anti-atrophic, anti-cachexia effect that may provide additional benefits to this potential therapy in heart failure.

PRPS2 Enhances Resistance to Cisplatin via Facilitating Exosomes-mediated Macrophage M2 Polarization in Non-small Cell Lung Cancer

Background: Phosphoribosyl pyrophosphate synthetases 2 (PRPS2) is reported as an oncogene in various cancers. However, the role of PRPS2 in cisplatin (DDP) resistance of non-small cell lung cancer (NSCLC) remains unclear. The present study aimed to explore the effect of PRPS2 in DDP resistance of NSCLC.Methods: mRNA expression levels of genes were detected by RT-PCR. Enzyme-linked immunosorbent assay (ELISA) and Western blot were used to detect protein expression levels. Cell viability was determined by the MTT assay and colony formation assay. Cell apoptosis was detected using nucleosome ELISA assay and caspase-3 activity assay. PRPS2 silencing was achieved using siRNA transfection. Exosomes of cultured cells were isolated through ultracentrifugation.Results: Elevated PRPS2 was correlated with DDP resistance and poor prognosis in NSCLC patients. PRPS2 silencing enhanced sensitivity of DDP-resistant cells to DDP treatment. NSCLC cell-derived exosome induced M2 macrophage polarization. PRPS2 was enriched in the exosomes of NSCLC cells. Exosomal PRPS2 mediated M2 macrophage polarization to promote DDP resistance of NSCLC cells.Conclusions: In conclusion, PRPS2 potentiates resistance to DDP by promoting exosome-mediated macrophage M2 polarization in NSCLC.

Quantitative Proteomic Analysis Revealed Broad Roles of N6-Methyladenosine in Heat Shock Response

As optimum temperature is essential for all living organisms, heat shock represents a challenging problem for their survival. Therefore, cellular response to heat shock is among the most extensively investigated stress response pathways; however, how the human proteome responds to heat shock has not been comprehensively investigated. In this study, we employed stable isotope labeling by amino acids in cell culture (SILAC), together with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, to fulfill an in-depth analysis of the alterations in the human proteome in M14 human melanoma cells in response to heat shock stress. We found that, after heat shock, 284 and 278 out of the 4319 quantified proteins were with substantially diminished and elevated expressions, respectively. We also examined the alterations in human kinome after heat shock by using our recently developed targeted proteomic method relying on parallel-reaction monitoring. Our results showed that the expression levels of 11 and 22 kinase proteins were increased and decreased, respectively, by at least 1.5-fold upon heat shock. By interrogating publicly available RNA-seq and m⁶A sequencing data, we observed that the elevated expression of more than 30 proteins, including CHEK1 and CCND3 kinases, could occur via an m⁶A-mediated mechanism. Furthermore, our results from single-base elongation and ligation-based quantitative polymerase chain reaction (qPCR) amplification (SELECT) and luciferase reporter assays revealed that heat shock gave rise to elevated m⁶A levels at A280 and A286 sites in the 5'-untranslated region of HSPH1 mRNA, thereby leading to increased translation of HSPH1 protein. Together, our discovery and targeted proteomic methods revealed the reprogramming of human proteome and kinome upon heat shock stress and provided insights into cellular responses toward heat shock stress.

Targeted Proteomic Analysis Revealed Kinome Reprogramming during Acquisition of Radioresistance in Breast Cancer Cells

Radiotherapy constitutes a major therapeutic modality for early management of breast cancer. Despite the high efficacy in treating breast cancer (BC), radiation resistance and tumor recurrence are major hurdles in breast cancer radiotherapy. Herein, stable isotope labeling by amino acids in cell culture (SILAC) was employed, along with the parallel-reaction monitoring (PRM)-based targeted quantitative proteomic method, to examine the differences in kinase protein expression in MCF-7 and MDA-MB-231 breast cancer cells and their corresponding radioresistant C6 and C5 clones. We quantified the relative protein expression levels of 300 and 281 kinases in C5/MDA-MB-231 and C6/MCF-7 pairs of breast cancer cells, respectively. We also showed that TAF9, which was one of the differentially expressed kinases, enhances radiation resistance in breast cancer cells. Moreover, a correlation analysis of gene expression suggested TAF9's role in upregulating the expression of genes involved with radioresistance. Overall, our study uncovered a large number of differentially expressed kinases accompanied with the acquisition of radioresistance and revealed a role of TAF9 in promoting radioresistance in breast cancer.

Role of PRPS2 as a prognostic and therapeutic target in osteosarcoma

AIMS

Osteosarcoma (OS) is the most common primary malignant tumour of the bone. However, further improvement in survival has not been achieved due to a lack of well-validated prognostic markers and more effective therapeutic agents. Recently, the c-Myc-phosphoribosyl pyrophosphate synthetase 2 (PRPS2) pathway has been shown to promote nucleic acid metabolism and cancer cell proliferation in malignant melanoma; phosphorylated mammalian target of rapamycin (p-mTOR) has been upregulated and an effective therapeutic target in OS. However, the p-mTOR-PRPS2 pathway has not been evaluated in OS.

METHODS

In this study, the expression level of PRPS2, p-mTOR and marker of proliferation (MKI-67) was observed in a cohort of specimens (including 236 OS cases and 56 control samples) using immunohistochemistry, and the association between expression level and clinicopathological characteristics of patients with OS was analysed.

RESULTS

PRPS2 protein level, which is related to tumour proliferation, was higher in OS cells (p=0.003) than in fibrous dysplasia, and the higher PRPS2 protein level was associated with a higher tumour recurrence (p=0.001). In addition, our statistical analysis confirmed that PRPS2 is a novel, independent prognostic indicator of OS. Finally, we found that the expression of p-mTOR was associated with the poor prognosis of patients with OS (p<0.05).

CONCLUSIONS

PRPS2 is an independent prognostic marker and a potential therapeutic target for OS.

Transcription Factor AP4 Mediates Cell Fate Decisions: To Divide, Age, or Die

Simple Summary

Here, we review the literature on Activating Enhancer-Binding Protein 4 (AP4)/transcription factor AP4 (TFAP4) function and regulation and its role in cancer. Elevated expression of AP4 was detected in tumors of various organs and is associated with poor patient survival. AP4 is encoded by a Myc target gene and mediates cell fate decisions by regulating multiple processes, such as cell proliferation, epithelial-mesenchymal transition, stemness, apoptosis, and cellular senescence. Thereby, AP4 may be critical for tumor initiation and progression. In this review article, we summarize published evidence showing how AP4 functions as a transcriptional activator and repressor of a plethora of direct target genes in various physiological and pathological conditions. We also highlight the complex interactions of AP4 with c-Myc, N-Myc, p53, lncRNAs, and miRNAs in feed-back loops, which control AP4 levels and mediate AP4 functions. In the future, a better understanding of AP4 may contribute to improved prognosis and therapy of cancer.

Abstract

Activating Enhancer-Binding Protein 4 (AP4)/transcription factor AP4 (TFAP4) is a basic-helix-loop-helix-leucine-zipper transcription factor that was first identified as a protein bound to SV40 promoters more than 30 years ago. Almost 15 years later, AP4 was characterized as a target of the c-Myc transcription factor, which is the product of a prototypic oncogene that is activated in the majority of tumors. Interestingly, AP4 seems to represent a central hub downstream of c-Myc and N-Myc that mediates some of their functions, such as proliferation and epithelial-mesenchymal transition (EMT). Elevated AP4 expression is associated with progression of cancer and poor patient prognosis in multiple tumor types. Deletion of AP4 in mice points to roles of AP4 in the control of stemness, tumor initiation and adaptive immunity. Interestingly, ex vivo AP4 inactivation results in increased DNA damage, senescence, and apoptosis, which may be caused by defective cell cycle progression. Here, we will summarize the roles of AP4 as a transcriptional repressor and activator of target genes and the contribution of protein and non-coding RNAs encoded by these genes, in regulating the above mentioned processes. In addition, proteins interacting with or regulating AP4 and the cellular signaling pathways altered after AP4 dysregulation in tumor cells will be discussed.

A Targeted Quantitative Proteomic Method Revealed a Substantial Reprogramming of Kinome during Melanoma Metastasis

Kinases are involved in numerous critical cell signaling processes, and dysregulation in kinase signaling is implicated in many types of human cancers. In this study, we applied a parallel-reaction monitoring (PRM)-based targeted proteomic method to assess kinome reprogramming during melanoma metastasis in three pairs of matched primary/metastatic human melanoma cell lines. Around 300 kinases were detected in each pair of cell lines, and the results showed that Janus kinase 3 (JAK3) was with reduced expression in the metastatic lines of all three pairs of melanoma cells. Interrogation of The Cancer Genome Atlas (TCGA) data showed that reduced expression of JAK3 is correlated with poorer prognosis in melanoma patients. Additionally, metastatic human melanoma cells/tissues exhibited diminished levels of JAK3 mRNA relative to primary melanoma cells/tissues. Moreover, JAK3 suppresses the migration and invasion of cultured melanoma cells by modulating the activities of matrix metalloproteinases 2 and 9 (MMP-2 and MMP-9). In summary, our targeted kinome profiling method provided by far the most comprehensive dataset for kinome reprogramming associated with melanoma progression, which builds a solid foundation for examining the functions of other kinases in melanoma metastasis. Moreover, our results reveal a role of JAK3 as a potential suppressor for melanoma metastasis.

High-Throughput Targeted Quantitative Analysis of the Interaction between HSP90 and Kinases

Kinases, which function in numerous cell signaling processes, are among the best characterized groups of client proteins for the 90-kDa heat shock protein (HSP90), a molecular chaperone that suppresses the aggregation and maintains the proper folding of its substrate proteins (i.e., clients). No high-throughput proteomic method, however, has been developed for the characterizations of the interactions between HSP90 and the human kinome. Herein, by employing a parallel-reaction monitoring (PRM)-based targeted proteomic method, we found that 99 out of the 249 detected kinase proteins display diminished expression in cultured human cells upon treatment with ganetespib, a small-molecule HSP90 inhibitor. PRM analysis of kinase proteins in the affinity pull-down samples showed that 86 out of the 120 detected kinases are enriched from the CRISPR-engineered cells where a tandem affinity tag was conjugated with the C-terminus of endogenous HSP90β protein over the parental cells. Together, our results from the two complementary quantitative proteomic experiments offer systematic characterizations about the HSP90-kinase interactions at the entire proteome scale and reveal extensive interactions between HSP90 and kinase proteins in human cells.

Parallel-Reaction-Monitoring-Based Proteome-Wide Profiling of Differential Kinase Protein Expression during Prostate Cancer Metastasis in Vitro

Prostate cancer is the most common type of cancer in men, and kinases are heavily pursued as drug targets for anticancer therapy. In this study, we applied our recently reported parallel-reaction-monitoring (PRM)-based targeted proteomic method to examine the reprogramming of the human kinome associated with bone metastasis of prostate cancer in vitro. The method displayed superior sensitivity over the shotgun-proteomic approach, and it facilitated the quantification of the relative expression of 276 kinase proteins in a pair of bone metastatic prostate cancer cells. Among the differentially expressed kinases, mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) stimulates the migration and invasion of cultured prostate cancer cells, partially by modulating the activity of secreted matrix metalloproteinases 9 (MMP-9). We also found that the upregulation of MAP4K4 in metastatic prostate cancer cells is driven by the MYC proto-oncogene. Cumulatively, we identify MAP4K4 as a potential promoter for prostate cancer metastasis in vitro.

Quantitative Interrogation of the Human Kinome Perturbed by Two BRAF Inhibitors

Oncogenic BRAF mutations contribute to the development of a number of cancers, and small-molecule BRAF inhibitors have been approved by the Food and Drug Administration (FDA) for anticancer therapy. In this study, we employed two targeted quantitative proteomics approaches for monitoring separately the alterations in protein expression and ATP binding affinities of kinases in cultured human melanoma cells elicited by two FDA-approved small-molecule BRAF inhibitors, dabrafenib and vemurafenib. Our results showed that treatment with the two inhibitors led to markedly different reprograming of the human kinome. Furthermore, we confirmed that vemurafenib could compromise the ATP binding capacity of MAP2K5 in vitro and inhibit its kinase activity in cells. Together, our targeted quantitative proteomic methods revealed profound changes in expression levels of kinase proteins in cultured melanoma cells upon treatment with clinically used BRAF inhibitors and led to the discovery of novel putative target kinases for these inhibitors.