Specificity Protein Phosphatase Research Articles

Protein Interaction Kinetics Delimit the Performance of Phosphorylation-Driven Protein Switches.

Post-translational modifications (PTMs) such as phosphorylation and dephosphorylation can rapidly alter protein surface chemistry and structural conformation, which can switch protein-protein interactions (PPIs) within signaling networks. Recently, de novo-designed phosphorylation-responsive protein switches have been created that harness kinase- and phosphatase-mediated phosphorylation to modulate PPIs. PTM-driven protein switches are promising tools for investigating PTM dynamics in living cells, developing biocompatible nanodevices, and engineering signaling pathways to program cell behavior. However, little is known about the physical and kinetic constraints of PTM-driven protein switches, which limits their practical application. In this study, we present a framework to evaluate two-component PTM-driven protein switches based on four performance metrics: effective concentration, dynamic range, response time, and reversibility. Our computational models reveal an intricate relationship between the binding kinetics, phosphorylation kinetics, and switch concentration that governs the sensitivity and reversibility of PTM-driven protein switches. Building upon the insights of the interaction modeling, we built and evaluated novel phosphorylation-driven protein switches consisting of phosphorylation-sensitive coiled coils as sensor domains fused to fluorescent proteins as actuator domains. By modulating the phosphorylation state of the switches with a specific protein kinase and phosphatase, we demonstrate fast, reversible transitions between "on" and "off" states. The response of the switches linearly correlated to the kinase concentration, demonstrating its potential as a biosensor for kinase measurements in real time. As intended, the switches responded to specific kinase activity with an increase in the fluorescence signal and our model could be used to distinguish between two mechanisms of switch activation: dimerization or a structural rearrangement. The protein switch kinetics model developed here should enable PTM-driven switches to be designed with ideal performance for specific applications.

The Impact of Calcium Depletion on Proliferation of Chlorella sorokiniana Strain DSCG150.

This study analyzed the effects of Ca2+ metal ions among culture medium components on the Chlorella sorokiniana strain DSCG150 strain cell growth. The C. sorokiniana strain DSCG150 strain grew based on a multiple fission cell cycle and growth became stagnant in the absence of metal ions in the medium, particularly Ca2+. Flow cytometry and confocal microscopic image analysis results showed that in the absence of Ca2+, cell growth became stagnant as the cells accumulated into four autospores and could not transform into daughter cells. Genetic analysis showed that the absence of Ca2+ caused upregulation of calmodulin (calA) and cell division control protein 2 (CDC2_1) genes, and downregulation of origin of replication complex subunit 6 (ORC6) and dual specificity protein phosphatase CDC14A (CDC14A) genes. Analysis of gene expression patterns by qRT-PCR showed that the absence of Ca2+ did not affect cell cycle progression up to 4n autospore, but it inhibited Chlorella cell fission (liberation of autospores). The addition of Ca2+ to cells cultivated in the absence of Ca2+ resulted in an increase in n cell population, leading to the resumption of C. sorokiniana growth. These findings suggest that Ca2+ plays a crucial role in the fission process in Chlorella.

Mechanistic Understanding of Dexamethasone-Mediated Protection against Remdesivir-Induced Hepatotoxicity.

Remdesivir (RDV), a broad-spectrum antiviral agent, is often used together with dexamethasone (DEX) for hospitalized COVID-19 patients requiring respiratory support. Potential hepatic adverse drug reaction is a safety concern associated with the use of RDV. We previously reported that DEX cotreatment effectively mitigates RDV-induced hepatotoxicity and reduces elevated serum alanine aminotransferase and aspartate aminotransferase levels in cultured human primary hepatocytes (HPH) and hospitalized COVID-19 patients, respectively. Yet, the precise mechanism behind this protective drug-drug interaction remains largely unknown. Here, we show that through the activation of p38, c-Jun N-terminal kinase (JNK), and extracellular signal-regulated kinases 1 and 2 (ERK1/2) signaling, RDV induces apoptosis (cleavage of caspases 8, 9, and 3), autophagy (increased autophagosome and LC3-II), and mitochondrial damages (decreased membrane potential, respiration, ATP levels, and increased expression of Bax and the released cytosolic cytochrome C) in HPH. Importantly, cotreatment with DEX partially reversed RDV-induced apoptosis, autophagy, and cell death. Mechanistically, DEX deactivates/dephosphorylates p38, JNK, and ERK1/2 signaling by enhancing the expression of dual specificity protein phosphatase 1 (DUSP1), a mitogen-activated protein kinase (MAPK) phosphatase, in a glucocorticoid receptor (GR)-dependent manner. Knockdown of GR in HPH attenuates DEX-mediated DUSP1 induction, MAPK dephosphorylation, as well as protection against RDV-induced hepatotoxicity. Collectively, our findings suggest a molecular mechanism by which DEX modulates the GR-DUSP1-MAPK regulatory axis to alleviate the adverse actions of RDV in the liver. SIGNIFICANCE STATEMENT: The research uncovers the molecular mechanisms by which dexamethasone safeguards against remdesivir-associated liver damage in the context of COVID-19 treatment.

Transcriptomic responses to drought stress in the Patagonian southern beech Nothofagus alpina

BackgroundDeciphering the genetic architecture of drought tolerance could allow the candidate genes identification responding to water stress. In the Andean Patagonian forest, the genus Nothofagus represents an ecologically relevant species to be included in different genomic studies. These studies are scarce in South American ecosystems however represent an important source of genomic data in order to interpret future climate-change environment scenarios of these emblematic forests. Here, we achieved the assemblage of the transcriptome of N. alpina while searching for key genes of activated or suppressed metabolic pathways in response to drought stress.ResultsDe novo transcriptome assembly resulted in 104,030 transcripts. Following confirmation of drought conditions, based on reduction of leaf water potential and stomatal conductance, a differential gene expression analysis resulted in 2720 significantly expressed genes (1601 up-regulated and 1119 down-regulated). Enrichment analysis (over-representation analysis and gene set enrichment analysis) resulted in more than one hundred stress-responsive term ontologies (i.e. biological processes) and pathways. Terms such as response to abscisic acid and pathways such as plant hormone signal transduction or starch and sucrose metabolism were over-represented. Protein–protein interaction assessment resulted in networks with significantly expressed top common hub gene clusters (e.g. plant-type cell wall biogenesis among down-regulated or ABA-signalling among up-regulated). These networks evidenced important regulators at gene expression such as transcriptional factors.ConclusionsResponses of N. alpina seedlings to drought stress were evidenced by the activation of several genes linked to GO biological processes and KEGG pathways, which were mainly based on over-expression of specific protein kinases, phosphatases, synthases and transcription factors. This suggests an up-regulation of signalling pathways, triggered through plant hormones such as abscisic acid or auxin, which could counteract the osmotic stress created as a probable immediate response to drought. On the other hand, groups of carbon fixation genes related to the galactose metabolism, photosynthesis, secondary wall biogenesis, and fatty acid biosynthesis degradation were down-regulated under drought. Overall, our results provide new genomic data for understanding how non-model long-lived trees of Patagonian forests would acclimate to environmental changes.

Abstract C081: The lysine demethylase KDM4C is an oncogenic driver in pancreatic ductal adenocarcinoma

Abstract Deregulation of proteins involved in chromatin regulation is common in pancreatic ductal adenocarcinoma (PDAC), occurring via both genomic and non-genomic mechanisms. Lysine demethylase 4C (KDM4C) is one of the chromatin-modifying proteins frequently overexpressed across multiple solid cancers. We observed upregulation of Kdm4c protein in a panel of human and murine PDAC cell lines, as well as in PDAC patient samples compared to non-neoplastic controls. CRISPR/Cas9-mediated deletion of KDM4C in human and murine PDAC cells resulted in reduced proliferation and clonogenicity, and increased survival of orthotopically implanted murine PDAC allografts. Notably, in multiple KDM4C-null PDAC clones analyzed by reverse phase protein arrays (RPPA), we observed downregulation of activated mitogen-activated protein kinase (MAP kinase) pathway components (including phospho-MEK and phospho-ERK), which are key effector pathways downstream of mutant KRAS. In vitro propagation of KDM4C-null PDAC lines eventually led to adaptation and restitution of MAP kinase signaling via compensatory upregulation of other KDM4 family members (KDM4A and KDM4B). In order to bypass genetic compensation by KDM4 family members, we utilized a preclinical grade pan-KDM4 inhibitor (TACH107, Tachyon Therapeutics) in PDAC cell lines, which confirmed profound reduction in proliferation and colony formation; in vivo xenograft and allograft studies with TACH107 are now ongoing. To characterize signaling pathways perturbed by KDM4C deregulation, we investigated the transcriptional changes in PDAC cells with and without KDM4C deletion by RNA-seq and integrated these with alterations in H3K9me3 and H3K36me3 marks using histone ChIP-Seq. Regulatory network analysis identified ATF4 as one of the top downregulated transcription factor networks, validating a previously published observation linking KDM4C to amino acid biosynthesis and cell proliferation. Gene set enrichment analysis showed downregulation of RAS signatures, consistent with the RPPA data on attenuation of MAP Kinase pathway. DUSP2, a member of the dual specificity protein phosphatase subfamily that inactivates ERK, is transcriptionally upregulated and has increased H3K36me3 marks near the promoter region in KDM4C-depleted cells, nominating it as a candidate of KDM4C-mediated epigenetic regulation. To further delineate the essential binding partners of KDM4C in chromatin regulation, we have created HA-tagged catalytic domain and reader domain deletion constructs that will be used for immunoprecipitation followed by mass spectrometry analysis. Overall, our data suggests that KDM4C - and other KDM4 family members – regulate MAPK signaling in KRAS-mutant cells, at least partially via attenuation of transcripts encoding specific protein phosphatases. To the best of our knowledge, this is the first demonstration linking the requirement of sustained activity of the KDM4 family of lysine demethylases to MAPK signaling in cancer and presents an opportunity to leverage this oncogenic pathway for therapeutic purposes. Citation Format: Menna-t-Allah Shaheen, Laila Barkoudeh, Sarah Dhebat, Kimal I. Rajapakshe, Bidyut Ghosh, Anirban Maitra. The lysine demethylase KDM4C is an oncogenic driver in pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr C081.

MID-LIFE PLASMA PROTEINS ASSOCIATE WITH PREFRAILTY AND FRAILTY: A PROTEOMIC ANALYSIS

Abstract Physical frailty is a syndrome that typically manifests in later life, although the pathogenic process causing physical frailty likely begins decades earlier. To date, few studies have examined the biological signatures in mid-life associated with frailty in late life. We evaluated 4955 plasma proteins (log 2-transformed and standardized) measured using the SomaScan platform among 3810 participants (57.8+/-5.0 years, 58.2% women) at Visit 3 of the Atherosclerosis Risk in Community (ARIC) study, and their frailty status across up to 3 study visits in late-life (median follow-up 19 years). We used multinomial logistic regression models to examine the associations between the protein levels and the frailty status, adjusting for demographics, health indicators, comorbidities, and follow-up time. Two sets of 2 proteins were identified to be associated with prefrailty and frailty, respectively, after Bonferroni correction (p< 1.01×10-5). Higher concentration of hydroxymethylglutaryl-CoA synthase (HMGCS1; OR=1.22), a regulator of cholesterol synthesis, and lower concentration of dual specificity protein phosphatase 13 isoform A (DUSP13A; OR=0.82), a protein involved in cell apoptosis, were associated with higher odds of prefrailty. Higher concentration of growth differentiation factor 15 (GDF15; OR=1.39), a protein related to inflammation and cell senescence, and lower concentration of contactin-1 (CNTN1; OR=0.72), a protein involved in nervous system development and signalling, were associated with higher odds of frailty. The pathway and upstream regulator analyses of the physical frailty- or prefrailty-associated proteins (p< 0.01) revealed the dysregulation of apoptosis, inflammation, and neuromuscular communication in mid-life. Our findings provides new insights into frailty etiology earlier in the life course.

ADSC secretome constrains NK cell activity by attenuating IL-2-mediated JAK-STAT and AKT signaling pathway via upregulation of CIS and DUSP4

BackgroundMesenchymal stem cells (MSCs) have immunomodulatory properties and therapeutic effects on autoimmune diseases through their secreted factors, referred to as the secretome. However, the specific key factors of the MSC secretome and their mechanisms of action in immune cells have not been fully determined. Most in vitro experiments are being performed using immune cells, but experiments using natural killer (NK) cells have been neglected, and a few studies using NK cells have shown discrepancies in results. NK cells are crucial elements of the immune system, and adjustment of their activity is essential for controlling various pathological conditions. The aim of this study was to elucidate the role of the adipose tissue-derived stem cell (ADSC) secretome on NK cell activity.MethodsTo obtain the ADSC secretome, we cultured ADSCs in medium and concentrated the culture medium using tangential flow filtration (TFF) capsules. We assessed NK cell viability and proliferation using CCK-8 and CFSE assays, respectively. We analyzed the effects of the ADSC secretome on NK cell activity and pathway-related proteins using a combination of flow cytometry, ELISA, cytotoxicity assay, CD107a assay, western blotting, and quantitative real-time PCR. To identify the composition of the ADSC secretome, we performed LC–MS/MS profiling and bioinformatics analysis. To elucidate the molecular mechanisms involved, we used mRNA sequencing to profile the transcriptional expression of human blood NK cells.ResultsThe ADSC secretome was found to restrict IL-2-mediated effector function of NK cells while maintaining proliferative potency. This effect was achieved through the upregulation of the inhibitory receptor CD96, as well as downregulation of activating receptors and IL-2 receptor subunits IL-2Rα and IL-2Rγ. These changes were associated with attenuated JAK-STAT and AKT pathways in NK cells, which were achieved through the upregulation of cytokine-inducible SH2-containing protein (CIS, encoded by Cish) and dual specificity protein phosphatase 4 (DUSP4). Furthermore, proteomic analysis revealed twelve novel candidates associated with the immunomodulatory effects of MSCs.ConclusionsOur findings reveal a detailed cellular outcome and regulatory mechanism of NK cell activity by the ADSC secretome and suggest a therapeutic tool for treating NK-mediated inflammatory and autoimmune diseases using the MSC secretome.

Negative Feedback Regulation of MAPK Signaling Is an Important Driver of CLL Progression

Chronic lymphocytic leukemia (CLL) represents approximately 25% of all new cases of leukemia in the USA. Insight into the pathogenesis of CLL has led to the development of highly effective treatments in the past decade. Nevertheless, CLL patients with activating mutations in the mitogen-activated protein kinase (MAPK) pathway, which enables cell proliferation and differentiation, comprise a distinct subgroup with poor clinical prognosis such as shorter treatment-free survival and higher drug resistance. Dual specificity protein phosphatases (DUSPs) negatively regulate MAPK signaling and are required to limit and terminate the activating signal. Whether DUSP signaling is crucial for the development and progression of MAPK driven CLL is unknown. Thus, in this study we investigated the expression and functional relevance of negative MAPK regulators DUSP1 and DUSP6 in CLL. Analyzing mRNA data sets of CLL patients, we discovered that DUSP1 and DUSP6 were broadly expressed in CLL. High expression levels of DUSP6, though not DUSP1, were found in cases with activating mutations within the MAPK pathway and correlated with a poor clinical outcome, indicated by shorter time-to-treatment and overall survival. To investigate the functional relevance of DUSP1- and DUSP6-mediated negative MAPK regulation in CLL, we tested the effects of the dual-specific DUSP1/6 inhibitor BCI on CLL cells. DUSP1/6 inhibition in vitro resulted in a dose-dependent induction of specific cell death of CLL cells, whereas B cells from healthy donors remained unaffected. Treatment of mice with an adoptively transferred murine CLL with an in vivo applicable derivate of BCI also significantly decreased CLL levels in the spleen and peritoneal cavity, compared to a vehicle treated control group. Further, CRISPR/Cas9-mediated knockout of DUSP1 or DUSP6 in the CLL cell line MEC-1 reduced cell proliferation and fitness; however, DUSP1/6 double knockouts lead to syngeneic lethality. Thus, DUSP1 and DUSP6 are crucial for negative MAPK pathway regulation to enable cell survival. To assess changes in intracellular signaling pathways after DUSP1/6 inhibition, we performed a phospho-proteome analysis of BCI treated patient-derived CLL cells and compared them to vehicle treated cells. As expected, a significant deregulation of B-cell receptor and MAPK signaling was detected after inhibition, with an increase in the activating phosphorylation on ERK1 and ERK2, which are targeted by DUSP1/6, confirming on-target specificity of BCI using an unbiased approach. To gain insight into the mechanism driving cell death, we conducted a BCI time course analysis followed by a phospho-proteome screen and observed that the DNA damage response (DDR) and the apoptosis pathway were among the strongest regulated pathways upon DUSP1/6 inhibition in MEC-1 cells. To validate these findings, we used immunoblotting and detected phosphorylation of DDR key molecules, such as ATF2 and c-JUN, in human CLL samples after DUSP1/6 inhibition. We also used flow cytometry to confirm acute activation of the MAPK pathway after BCI treatment by detecting increased phospho-γH2AX (DNA damage) and phosphatidylserine (apoptosis) levels. Furthermore, we showed that the apoptotic cell death is promoted by CHK1/2 kinases and depends on MAPK activity. Chemotherapeutic drug resistances are often detected in patients with deletion of p53 or ATM, central regulators of the DDR. Hence, we tested the effectiveness of DUSP1/6 inhibition on patient derived CLLs carrying a loss of function variation of p53 or ATM. We did not detect a significant difference in cytotoxicity, indicating DUSP1/6 inhibition effectively decreases CLL viability, even in cases without functional p53/ATM-mediated DDR. Finally, we generated a MEC-1 cell line resistant to the chemotherapeutic agent idelalisib, as a model for drug resistant CLLs. As the sensitivity to idelalisib decreased, the cells became more sensitive to BCI. When comparing the effects of BCI on CLL cells from treatment naïve patients compared to ibrutinib-refractory patients, we found no differences in sensitivity to DUSP1/6 inhibition. In conclusion, we show that MAPK deregulation by DUSP1/6 inhibition is highly effective to induce cytotoxic cell death in CLL cells, even without functional p53/ATM-mediated DDR; hence, we suggest DUSP1/6 inhibition is a promising approach to treat drug resistant and refractory CLLs. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Screening of genes encoding proteins that interact with ISG15: Probing a cDNA library from a snakehead fish cell line using a yeast two-hybrid system

Interferon-stimulated gene 15 (ISG15) regulates cellular life processes, including defense responses against infection by a variety of viral pathogens, by binding to target proteins. At present, various fish ISG15s have been identified, but the biological function of ISG15 in snakehead fish is still unclear. In this study, total RNA was extracted from snakehead fish cell line E11, ds cDNA was synthesized and purified using SMART technology, and the resulting cDNA library was screened by co-transforming yeast cells. The library titer was 4.28 × 109 CFU/mL. Using snakehead ISG15 as the bait protein, the recombinant bait vector pGBKT7-ISG15 was constructed and transformed into the yeast strain Y2HGold. The toxicity and self-activation activity of the bait vector were detected on the deficient medium, and the prey proteins interacting with ISG15 were screened. In total, 19 interacting proteins of ISG15 were identified, including mitotic checkpoint protein BUB3, hypothetical protein SnRVgp6, elongation factor 1-beta, 60S ribosomal protein L9, dual specificity protein phosphatase 5-like, eukaryotic translation initiation factor 3 subunit I and ferritin. A yeast spotting assay further probed the interaction between ISG15 and DUSP5. These results increase our understanding of the interaction network of snakehead ISG15 and will aid in exploring the underlying mechanisms of snakehead ISG15 functions in the future.

Combined Dusp4 and p53 loss with Dbf4 amplification drives tumorigenesis via cell cycle restriction and replication stress escape in breast cancer

AimDeregulated signaling pathways are a hallmark feature of oncogenesis and driver of tumor progression. Dual specificity protein phosphatase 4 (DUSP4) is a critical negative regulator of the mitogen-activated protein kinase (MAPK) pathway and is often deleted or epigenetically silenced in tumors. DUSP4 alterations lead to hyperactivation of MAPK signaling in many cancers, including breast cancer, which often harbor mutations in cell cycle checkpoint genes, particularly in TP53.MethodsUsing a genetically engineered mouse model, we generated mammary-specific Dusp4-deleted primary epithelial cells to investigate the necessary conditions in which DUSP4 loss may drive breast cancer oncogenesis.ResultsWe found that Dusp4 loss alone is insufficient in mediating tumorigenesis, but alternatively converges with loss in Trp53 and MYC amplification to induce tumorigenesis primarily through chromosome 5 amplification, which specifically upregulates Dbf4, a cell cycle gene that promotes cellular replication by mediating cell cycle checkpoint escape.ConclusionsThis study identifies a novel mechanism for breast tumorigenesis implicating Dusp4 loss and p53 mutations in cellular acquisition of Dbf4 upregulation as a driver of cellular replication and cell cycle checkpoint escape.

Effect of miR-101 on the Proliferation and Apoptosis of Goat Hair Follicle Stem Cells.

The Yangtze River Delta white goat is a rare goat species capable of producing high-quality brush hair. Dual specificity protein phosphatase 1 (DUSP1) may play a role in the formation of high-quality brush hair, as evidenced by our previous research. We investigated the potential mechanisms that regulate the proliferation and apoptosis of goat hair follicle stem cells. We particularly focused on the relationship between DUSP1 and miR-101, which directly targets DUSP1, predicted and screened through bioinformatics websites. Then, fluorescence assays, flow cytometry, RT-qPCR, and Western blotting were used to investigate the effects of miR-101 on the proliferation and apoptosis of hair follicle stem cells. We found that miR-101 overexpression significantly decreased (p < 0.01) apoptosis and promoted the proliferation of hair follicle stem cells. Furthermore, the overexpression of miR-101 increased (p < 0.05) the mRNA and protein expression levels of the proliferation-related gene (PCNA) and anti-apoptotic gene (Bcl-2), and it decreased (p < 0.05) the mRNA and protein expression levels of the apoptotic gene (Bax). In conclusion, miR-101 can promote the proliferation of and inhibit the apoptosis of hair follicle stem cells by targeting DUSP1, which provides a theoretical basis for further elucidating the molecular mechanism that regulates the production of high-quality brush hair of Yangtze River Delta white goats.

A conserved module regulates receptor kinase signalling in immunity and development.

Ligand recognition by cell-surface receptors underlies development and immunity in both animals and plants. Modulating receptor signalling is critical for appropriate cellular responses but the mechanisms ensuring this are poorly understood. Here, we show that signalling by plant receptors for pathogen-associated molecular patterns (PAMPs) in immunity and CLAVATA3/EMBRYO SURROUNDING REGION-RELATED peptides (CLEp) in development uses a similar regulatory module. In the absence of ligand, signalling is dampened through association with specific type-2C protein phosphatases. Upon activation, PAMP and CLEp receptors phosphorylate divergent cytosolic kinases, which, in turn, phosphorylate the phosphatases, thereby promoting receptor signalling. Our work reveals a regulatory circuit shared between immune and developmental receptor signalling, which may have broader important implications for plant receptor kinase-mediated signalling in general.

Valproic acid decreases vascular smooth muscle cell proliferation via protein phosphatase 2A-mediated p70 S6 kinase inhibition

Valproic acid (VPA) has been used to treat epilepsy and bipolar disorder. Although the abnormal proliferation of vascular smooth muscle cells (VSMCs) is a well-established contributor to the development of various vascular diseases including atherosclerosis, the effect of VPA on VSMC proliferation and its mechanism of action have not been fully revealed. Herein, we investigated the molecular mechanism by which VPA inhibits rat VSMC proliferation. VPA dose-dependently decreased VSMC proliferation, which was accompanied by the dose-dependent decrease in phosphorylation of p70 S6 kinase (p70S6K) at Thr389 (p-p70S6K-Thr389), and overexpression of the p70S6K-T389E mutant gene significantly reversed VPA-inhibited VSMC proliferation. Co-treatment with okadaic acid, a specific protein phosphatase 2A (PP2A) inhibitor, significantly restored p-p70S6K-Thr389. Furthermore, knockdown of PP2Ac gene expression by siRNA significantly reversed VPA-inhibited p-p70S6K-Thr389 and VSMC proliferation. Confocal microscopic analyses and co-immunoprecipitation results clearly showed that the physical binding of p70S6K and PP2Ac was promoted by VPA. Valpromide, a VPA's structural derivative with no histone deacetylase (HDAC) inhibition activity, as well as VPA and sodium butyrate, an HDAC inhibitor similar to VPA, decreased VSMC proliferation and p-p70S6K-Thr389, indicating that HDAC is not involved in VPA-inhibited VSMC proliferation. Finally, the inhibitory effects of VPA on p-p70S6K-Thr389 and VSMC proliferation were reiterated in a platelet-derived growth factor (PDGF)-induced in vitro atherosclerosis model. In conclusion, our results demonstrate that VPA decreased cell proliferation via PP2A-mediated inhibition of p-p70S6K-Thr389 in basal and PDGF-stimulated VSMCs. The results suggest that VPA could be used in the treatment and prevention of atherosclerosis and in-stent restenosis.

Dusp26 phosphatase regulates mitochondrial respiration and oxidative stress and protects neuronal cell death.

The dual specificity protein phosphatases (Dusps) control dephosphorylation of mitogen-activated protein kinases (MAPKs) as well as other substrates. Here, we report that Dusp26, which is highly expressed in neuroblastoma cells and primary neurons is targetedtothe mitochondrial outermembrane via its NH2-terminal mitochondrial targeting sequence. Loss of Dusp26 has asignificant impact on mitochondrial function that is associated with increased levels of reactive oxygen species (ROS), reduction in ATP generation, reduction in mitochondria motility and release of mitochondrial HtrA2 protease into the cytoplasm. The mitochondrial dysregulation in dusp26-deficient neuroblastoma cells leads to the inhibition of cell proliferation and cell death. In vivo, Dusp26 is highly expressed in neurons in different brain regions, including cortex and midbrain (MB). Ablation of Dusp26 in mouse model leads to dopaminergic (DA) neuronal cell loss in the substantia nigra par compacta (SNpc), inflammatory response in MB and striatum, and phenotypes that are normally associated with Neurodegenerative diseases. Consistent with the data fromour mouse model, Dusp26 expressing cells are significantly reduced in the SNpc of Parkinson's Disease patients. The underlying mechanism of DA neuronal death is that loss of Dusp26 in neurons increases mitochondrial ROS and concurrent activation of MAPK/p38 signaling pathway and inflammatory response. Our results suggest that regulation of mitochondrial-associated protein phosphorylation is essential for the maintenance of mitochondrial homeostasis and dysregulation of this process may contribute to the initiation and development of neurodegenerative diseases.

The beneficial effect of salubrinal on neuroinflammation and neuronal loss in intranigral LPS-induced hemi-Parkinson disease model in rats

Objective Endoplasmic reticulum stress (ERS) and neuroinflammation are triggers for neurodegenerative disorders. Salubrinal is a selective inhibitor of protein phosphatase 1 (PP1) complex involving dephosphorylation of phosphorylated eukaryotic initiation factor-2α (eIF2α), the key crucial pathway in the ERS. Therefore, this study assessed the effects of inhibition of the ERS with salubrinal in the intranigral hemi-Parkinson disease (PD) model. Materials and methods Animals were treated with salubrinal for one week after the PD model was created by intranigral lipopolysaccharide (LPS) administration. Apomorphine-induced rotation, rotarod, cylinder, and pole tests were performed to evaluate behavioral changes. Proinflammatory cytokines and the expression level of the dual specificity protein phosphatase 2 (DUSP2), PP1, and p-eIF2α were evaluated. Nigral expression of inducible nitric oxide synthase (iNOS), nuclear factor kappaB (Nf-κB), and cyclooxygenase (COX)-2 was determined. Finally, tyrosine hydroxylase and caspase-3/ caspase-9 expressions were assessed by immunohistochemistry. Results Salubrinal reduced the motor impairments and dopamine-related behavioral deficiencies caused by the LPS. Salubrinal attenuated the LPS-induced increased levels of interleukin (IL)-1β, IL-6, tumor necrosis factor-α, and salubrinal rescued the loss of TH expression and dopamine levels and prevented the caspase-3/9 increase in the substantial nigra (SN). LPS potently increased iNOS, Nf-κB, and COX-2 expression, but this effect was reduced after salubrinal treatment. Additionally, salubrinal attenuated the LPS-induced PP1 and DUSP2 increase. Conclusion Our results reveal that salubrinal is attenuating several inflammatory mediators and thereby decreased the inflammatory effects of LPS in the neurons of the SN. Together this results in increased cellular survival and maintained integrity of SN. Taken together our data show the beneficial effects of inhibition of ERS to restrict neuroinflammatory progression and neuronal loss in a PD model.

DUSP4 alleviates LPS-induced chondrocyte injury in knee osteoarthritis via the MAPK signaling pathway.

Knee osteoarthritis (KOA) is characterized by cartilage damage, and the associated pathogenesis is complex. The expression of dual specificity protein phosphatase 4 (DUSP4) is significantly decreased in osteoarthritis (OA); however, the specific role and mechanism underlying DUSP4 in OA are yet to be elucidated. ATDC5 cells were treated with lipopolysaccharide (LPS) to establish the cell injury model. The expression levels of DUSP4 were decreased in OA chondrocytes, demonstrated by reverse transcription-quantitative PCR and western blot analysis. Following overexpression of DUSP4 by cell transfection, Cell Counting Kit-8, ELISA, TUNEL and western blotting assays were used to detect the cell viability, oxidative stress, inflammation and apoptosis levels of LPS-induced ATDC5 cells. Overexpression of DUSP4 inhibited the activation of the MAPK signaling pathway, thereby reducing oxidative stress levels, inflammatory response and apoptosis in the OA cell model. The mechanisms underlying DUSP4 in OA were further explored following the addition of MAPK signaling pathway agonist, phorbol 12-myristate 13-acetate (PMA). The addition of PMA reversed the inhibitory effects of DUSP4 overexpression on oxidative stress, inflammatory response and apoptosis in cells. In summary, DUSP4 alleviated LPS-induced chondrocyte injury in KOA via the MAPK signaling pathway.

PP-1β and PP-2Aα modulate cAMP response element-binding protein (CREB) functions in aging control and stress response through de-regulation of αB-crystallin gene and p300-p53 signaling axis.

The function of the transcription factor, cAMP response element‐binding protein (CREB), is activated through S133 phosphorylation by PKA and others. Regarding its inactivation, it is not well defined. cAMP response element‐binding protein plays an essential role in promoting cell proliferation, neuronal survival and the synaptic plasticity associated with long‐term memory. Our recent studies have shown that CREB is an important player in mediating stress response. Here, we have demonstrated that CREB regulates aging process through suppression of αB‐crystallin and activation of the p300‐p53‐Bak/Bax signaling axis. First, we determined that two specific protein phosphatases, PP‐1β and PP‐2Aα, can inactivate CREB through S133 dephosphorylation. Subsequently, we demonstrated that cells expressing the S133A‐CREB, a mutant mimicking constant dephosphorylation at S133, suppress CREB functions in aging control and stress response. Mechanistically, S133A‐CREB not only significantly suppresses CREB control of αB‐crystallin gene, but also represses CREB‐mediated activation of p53 acetylation and downstream Bak/Bax genes. cAMP response element‐binding protein suppression of αB‐crystallin and its activation of p53 acetylation are major molecular events observed in human cataractous lenses of different age groups. Together, our results demonstrate that PP‐1β and PP‐2Aα modulate CREB functions in aging control and stress response through de‐regulation of αB‐crystallin gene and p300‐p53‐Bax/Bak signaling axis, which regulates human cataractogenesis in the aging lens.

Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9

BackgroundThe autonomous retroelement Long Interspersed Element-1 (LINE-1) mobilizes though a copy and paste mechanism using an RNA intermediate (retrotransposition). Throughout human evolution, around 500,000 LINE-1 sequences have accumulated in the genome. Most of these sequences belong to ancestral LINE-1 subfamilies, including L1PA2-L1PA7, and can no longer mobilize. Only a small fraction of LINE-1 sequences, approximately 80 to 100 copies belonging to the L1Hs subfamily, are complete and still capable of retrotransposition. While silenced in most cells, many questions remain regarding LINE-1 dysregulation in cancer cells.ResultsHere, we optimized CRISPR Cas9 gRNAs to specifically target the regulatory sequence of the L1Hs 5’UTR promoter. We identified three gRNAs that were more specific to L1Hs, with limited binding to older LINE-1 sequences (L1PA2-L1PA7). We also adapted the C-BERST method (dCas9-APEX2 Biotinylation at genomic Elements by Restricted Spatial Tagging) to identify LINE-1 transcriptional regulators in cancer cells. Our LINE-1 C-BERST screen revealed both known and novel LINE-1 transcriptional regulators, including CTCF, YY1 and DUSP1.ConclusionOur optimization and evaluation of gRNA specificity and application of the C-BERST method creates a tool for studying the regulatory mechanisms of LINE-1 in cancer. Further, we identified the dual specificity protein phosphatase, DUSP1, as a novel regulator of LINE-1 transcription.

Dephosphorylation of annexin A2 by protein phosphatase 1 regulates endothelial cell barrier.

Annexin A2 (ANXA2) is a multifunctional protein expressed in nearly all human tissues and cell types, playing a role in various signaling pathways. It is subjected to phosphorylation, but no specific protein phosphatase has been identified in its posttranslational regulation yet. Using pull-down assay followed by liquid chromatography-mass spectrometry analysis we found that ANXA2 interacts with TIMAP (TGF-beta-inhibited membrane-associated protein) in pulmonary artery endothelial cells. TIMAP is highly expressed in endothelial cells, where it acts as a regulatory and targeting subunit of protein phosphatase 1 (PP1). TIMAP plays an important role in the regulation of the endothelial barrier maintenance through the dephosphorylation of its several substrate proteins. In the present work, phosphorylation of Ser25 side chain in ANXA2 by protein kinase C (PKC) was shown both in vivo and in vitro. Phosphorylation level of ANXA2 at Ser25 increased greatly by inhibition of PP1 and by depletion of its regulatory subunit, TIMAP, implying a role of this PP1 holoenzyme in the dephosphorylation of ANXA2. Immunofluorescence staining and subcellular fractionations revealed a diffuse subcellular localization for the endogenous ANXA2, but phospho-Ser25 ANXA2 was mainly detected in the membrane. ANXA2 depletion lowered the basal endothelial barrier and inhibited cell migration, but had no significant effect on cell proliferation or viability. ANXA2 depleted cells failed to respond to PMA treatment, indicating an intimately involvement of phospho-ANXA2 in PKC signaling. Moreover, phosphorylation of ANXA2 disrupted its interaction with S100A10 suggesting a phosphorylation dependent multiple regulatory role of ANXA2 in endothelial cells. Our results demonstrate the pivotal role of PKC-ANXA2-PP1 pathway in endothelial cell signaling, especially in barrier function and cell migration.

DUSP12 regulates the tumorigenesis and prognosis of hepatocellular carcinoma

BackgroundDual specificity protein phosphatase (DUSP)12 is an atypical member of the protein tyrosine phosphatase family, which are overexpressed in multiple types of malignant tumors. This protein family protect cells from apoptosis and promotes the proliferation and motility of cells. However, the pathological role of DUSP12 in hepatocellular carcinoma (HCC) is incompletely understood.MethodsWe analyzed mRNA expression of DUSP12 between HCC and normal liver tissues using multiple online databases, and explored the status of DUSP12 mutants using the cBioPortal database. The correlation between DUSP12 expression and tumor-infiltrating immune cells was demonstrated using the Tumor Immune Estimation Resource database and the Tumor and Immune System Interaction Database. Loss of function assay was utilized to evaluate the role of DUSP12 in HCC progression.ResultsDUSP12 had higher expression along with mRNA amplification in HCC tissues compared with those in normal liver tissues, which suggested that higher DUSP12 expression predicted shorter overall survival. Analyses of functional enrichment of differentially expressed genes suggested that DUSP12 regulated HCC tumorigenesis, and that knockdown of DUSP12 expression by short hairpin (sh)RNA decreased the proliferation and migration of HCC cells. Besides, DUSP12 expression was positively associated with the infiltration of cluster of differentiation (CD)4+ T cells (especially CD4+ regulatory T cells), macrophages, neutrophils and dendritic cells. DUSP12 expression was positively associated with immune-checkpoint moieties, and was downregulated in a C3 immune-subgroup of HCC (which had the longest survival).ConclusionThese data suggest that DUSP12 may have a critical role in the tumorigenesis, infiltration of immune cells, and prognosis of HCC.