Protein-protein interactions in the regulation of the extracellular signal-regulated kinase

ELK1 inhibition alleviates amyloid pathology and memory decline by promoting the SYVN1-mediated ubiquitination and degradation of PS1 in Alzheimer's disease

ELK1 is a member of the E-twenty-six transcription factor family and is usually activated by phosphorylation at Ser383 and Ser389 by extracellular signal-regulated kinase 1/2 (ERK1/2). Dysregulation of ERK1/2 is involved in Alzheimer's disease (AD)-related neuropathogenesis and cognitive impairments. However, the role of ELK1 in AD pathogenesis remains unclear. Here we report that the expression of ELK1 was significantly increased in the brain tissues of patients with AD and AD model mice. The genetic knockdown of ELK1 or inhibition of its phosphorylation by an interfering peptide (TAT-DEF-ELK1 (TDE)) reduced amyloidogenic processing of APP by targeting PS1, consequently inhibiting Aβ generation and alleviating synaptic and memory impairments in APP23/PS45 double-transgenic AD model mice. In addition, we further found that ELK1 regulated the expression of PS1 by competitively inhibiting the interaction between PS1 and its E3 ubiquitin ligase synoviolin (SYVN1), thereby inhibiting the SYVN1-mediated ubiquitination and degradation of PS1. Our results demonstrate that ELK1 aberrantly increases in AD and genetic or pharmacological inhibition of ELK1 can alleviate AD-related pathology and memory impairments by enhancing the SYVN1-mediated PS1 ubiquitination and degradation, indicating that ELK1 may be a novel target for AD treatment.

CSM-Potential2: A comprehensive deep learning platform for the analysis of protein interacting interfaces

Proteins are molecular machinery that participate in virtually all essential biological functions within the cell, which are tightly related to their 3D structure. The importance of understanding protein structure-function relationship is highlighted by the exponential growth of experimental structures, which has been greatly expanded by recent breakthroughs in protein structure prediction, most notably RosettaFold, and AlphaFold2. These advances have prompted the development of several computational approaches that leverage these data sources to explore potential biological interactions. However, most methods are generally limited to analysis of single types of interactions, such as protein-protein or protein-ligand interactions, and their complexity limits the usability to expert users. Here we report CSM-Potential2, a deep learning platform for the analysis of binding interfaces on protein structures. In addition to prediction of protein-protein interactions binding sites and classification of biological ligands, our new platform incorporates prediction of interactions with nucleic acids at the residue level and allows for ligand transplantation based on sequence and structure similarity to experimentally determined structures. We anticipate our platform to be a valuable resource that provides easy access to a range of state-of-the-art methods to expert and non-expert users for the study of biological interactions. Our tool is freely available as an easy-to-use web server and API available at https://biosig.lab.uq.edu.au/csm_potential.

Graph masked self-distillation learning for prediction of mutation impact on protein-protein interactions

Assessing mutation impact on the binding affinity change (ΔΔG) of protein-protein interactions (PPIs) plays a crucial role in unraveling structural-functional intricacies of proteins and developing innovative protein designs. In this study, we present a deep learning framework, PIANO, for improved prediction of ΔΔG in PPIs. The PIANO framework leverages a graph masked self-distillation scheme for protein structural geometric representation pre-training, which effectively captures the structural context representations surrounding mutation sites, and makes predictions using a multi-branch network consisting of multiple encoders for amino acids, atoms, and protein sequences. Extensive experiments demonstrated its superior prediction performance and the capability of pre-trained encoder in capturing meaningful representations. Compared to previous methods, PIANO can be widely applied on both holo complex structures and apo monomer structures. Moreover, we illustrated the practical applicability of PIANO in highlighting pathogenic mutations and crucial proteins, and distinguishing de novo mutations in disease cases and controls in PPI systems. Overall, PIANO offers a powerful deep learning tool, which may provide valuable insights into the study of drug design, therapeutic intervention, and protein engineering.

The mechanism and potential therapeutic target of piezo channels in pain

Pain is a common symptom of many clinical diseases; it adversely affects patients' physical and mental health, reduces their quality of life, and heavily burdens patients and society. Pain treatment is one of the most difficult problems today. There is an urgent need to explore the potential factors involved in the pathogenesis of pain to improve its diagnosis and treatment rate. Piezo1/2, a newly identified mechanosensitive ion channel opens in response to mechanical stimuli and plays a critical role in regulating pain-related diseases. Inhibition or downregulation of Piezo1/2 alleviates disease-induced pain. Therefore, in this study, we comprehensively discussed the biology of this gene, focusing on its potential relevance in pain-related diseases, and explored the pharmacological effects of drugs using this gene for the treatment of pain.

SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein-protein complexes

MOTIVATION

Mutations in protein-protein interactions can affect the corresponding complexes, impacting function and potentially leading to disease. Given the abundance of membrane proteins, it is crucial to assess the impact of mutations on the binding affinity of these proteins. Although several methods exist to predict the binding free energy change due to mutations in protein-protein complexes, most require structural information of the protein complex and are primarily trained on the SKEMPI database, which is composed mainly of soluble proteins.

RESULTS

A novel sequence-based method (SAAMBE-MEM) for predicting binding free energy changes (ΔΔG) in membrane protein-protein complexes due to mutations has been developed. This method utilized the MPAD database, which contains binding affinities for wild-type and mutant membrane protein complexes. A machine learning model was developed to predict ΔΔG by leveraging features such as amino acid indices and position-specific scoring matrices (PSSM). Through extensive dataset curation and feature extraction, SAAMBE-MEM was trained and validated using the XGBoost regression algorithm. The optimal feature set, including PSSM-related features, achieved a Pearson correlation coefficient of 0.64, outperforming existing methods trained on the SKEMPI database. Furthermore, it was demonstrated that SAAMBE-MEM performs much better when utilizing evolution-based features in contrast to physicochemical features.

AVAILABILITY AND IMPLEMENTATION

The method is accessible via a web server and standalone code at http://compbio.clemson.edu/SAAMBE-MEM/. The cleaned MPAD database is available at the website.

Cpeb4-mediated Dclk2 promotes neuronal pyroptosis induced by chronic cerebral ischemia through phosphorylation of Ehf

Chronic cerebral ischemia (CCI) is a clinical syndrome characterised by brain dysfunction due to decreased chronic cerebral perfusion. CCI initiates several inflammatory pathways, including pyroptosis. RNA-binding proteins (RBPs) play important roles in CCI. This study aimed to explore whether the interaction between RBP-Cpeb4 and Dclk2 affected Ehf phosphorylation to regulate neuronal pyroptosis. HT22 cells and mice were used to construct oxygen glucose deprivation (OGD)/CCI models. We found that Cpeb4 and Dclk2 were upregulated in OGD-treated HT22 cells and CCI-induced hippocampal CA1 tissues. Cpeb4 upregulated Dclk2 expression by increasing Dclk2 mRNA stability. Knockdown of Cpeb4 or Dclk2 inhibited neuronal pyroptosis in OGD-treated HT22 cells and CCI-induced hippocampal CA1 tissues. By binding to the promoter regions of Caspase1 and Caspase3, the transcription factor Ehf reduced their promoter activities and inhibited the transcription. Dclk2 phosphorylated Ehf and changed its nucleoplasmic distribution, resulting in the exit of p-Ehf from the nucleus and decreased Ehf levels. It promoted the expression of Caspase1 and Caspase3 and stimulated neuronal pyroptosis of HT22 cells induced by OGD. Cpeb4/Dclk2/Ehf pathway plays an important role in the regulation of cerebral ischemia-induced neuronal pyroptosis.

CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by TTN Truncation Variants

BACKGROUND

TTN truncation variants (TTNtvs) are the most common genetic lesion identified in individuals with dilated cardiomyopathy, a disease with high morbidity and mortality rates. TTNtvs reduce normal TTN (titin) protein levels, produce truncated proteins, and impair sarcomere content and function. Therapeutics targeting TTNtvs have been elusive because of the immense size of TTN, the rarity of specific TTNtvs, and incomplete knowledge of TTNtv pathogenicity.

METHODS

We adapted CRISPR activation using dCas9-VPR to functionally interrogate TTNtv pathogenicity and develop a therapeutic in human cardiomyocytes and 3-dimensional cardiac microtissues engineered from induced pluripotent stem cell models harboring a dilated cardiomyopathy-associated TTNtv. We performed guide RNA screening with custom TTN reporter assays, agarose gel electrophoresis to quantify TTN protein levels and isoforms, and RNA sequencing to identify molecular consequences of TTN activation. Cardiomyocyte epigenetic assays were also used to nominate DNA regulatory elements to enable cardiomyocyte-specific TTN activation.

RESULTS

CRISPR activation of TTN using single guide RNAs targeting either the TTN promoter or regulatory elements in spatial proximity to the TTN promoter through 3-dimensional chromatin interactions rescued TTN protein deficits disturbed by TTNtvs. Increasing TTN protein levels normalized sarcomere content and contractile function despite increasing truncated TTN protein. In addition to TTN transcripts, CRISPR activation also increased levels of myofibril assembly-related and sarcomere-related transcripts.

CONCLUSIONS

TTN CRISPR activation rescued TTNtv-related functional deficits despite increasing truncated TTN levels, which provides evidence to support haploinsufficiency as a relevant genetic mechanism underlying heterozygous TTNtvs. CRISPR activation could be developed as a therapeutic to treat a large proportion of TTNtvs.

Cross-talk between zinc and calcium regulates ion transport: A role for the zinc receptor, ZnR/GPR39

Zinc is essential for many physiological functions, with a major role in digestive system, skin health, and learning and memory. On the cellular level, zinc is involved in cell proliferation and cell death. A selective zinc sensing receptor, ZnR/GPR39 is a Gq-coupled receptor that acts via the inositol trisphosphate pathway to release intracellular Ca2+. The ZnR/GPR39 serves as a mediator between extracellular changes in Zn2+ concentration and cellular Ca2+ signalling. This signalling pathway regulates ion transporters activity and thereby controls the formation of transepithelial gradients or neuronal membrane potential, which play a fundamental role in the physiological function of these tissues. This review focuses on the role of Ca2+ signalling, and specifically ZnR/GPR39, with respect to the regulation of the Na+/H+ exchanger, NHE1, and of the K+/Cl- cotransporters, KCC1-3, and also describes the physiological implications of this regulation.

The interplay of mitophagy, autophagy, and apoptosis in cisplatin-induced kidney injury: involvement of ERK signaling pathway

AKI induced by CP chemotherapy remains an obstacle during patient treatments. Extracellular signal-regulated protein kinases 1/2 (ERK), key participants in CP-induced nephrotoxicity, are suggested to be involved in the regulation of mitophagy, autophagy, and apoptosis. Human renal proximal tubular cells (HK-2) and BALB/cN mice were used to determine the role of ERK in CP-induced AKI. We found that active ERK is involved in cell viability reduction during apoptotic events but exerts a protective role in the early stages of treatment. Activation of ERK acts as a maintainer of the mitochondrial population and is implicated in mitophagy initiation but has no significant role in its conduction. In the late stages of CP treatment when ATP is deprived, general autophagy that requires ERK activation is initiated as a response, in addition to apoptosis activation. Furthermore, activation of ERK is responsible for the decrease in reserve respiratory capacity and controls glycolysis regulation during CP treatment. Additionally, we found that ERK activation is also required for the induction of NOXA gene and protein expression as well as FoxO3a nuclear translocation, but not for the regular ERK-induced phosphorylation of FoxO3a on Ser294. In summary, this study gives detailed insight into the involvement of ERK activation and its impact on key cellular processes at different time points during CP-induced kidney injury. Inhibitors of ERK activation, including Mirdametinib, are important in the development of new therapeutic strategies for the treatment of AKI in patients receiving CP chemotherapy.

Geometric Graph Learning to Predict Changes in Binding Free Energy and Protein Thermodynamic Stability upon Mutation

Accurate prediction of binding free energy changes upon mutations is vital for optimizing drugs, designing proteins, understanding genetic diseases, and cost-effective virtual screening. While machine learning methods show promise in this domain, achieving accuracy and generalization across diverse data sets remains a challenge. This study introduces Geometric Graph Learning for Protein-Protein Interactions (GGL-PPI), a novel approach integrating geometric graph representation and machine learning to forecast mutation-induced binding free energy changes. GGL-PPI leverages atom-level graph coloring and multiscale weighted colored geometric subgraphs to capture structural features of biomolecules, demonstrating superior performance on three standard data sets, namely, AB-Bind, SKEMPI 1.0, and SKEMPI 2.0 data sets. The model's efficacy extends to predicting protein thermodynamic stability in a blind test set, providing unbiased predictions for both direct and reverse mutations and showcasing notable generalization. GGL-PPI's precision in predicting changes in binding free energy and stability due to mutations enhances our comprehension of protein complexes, offering valuable insights for drug design endeavors.

A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions

Protein-protein interactions (PPIs) are essential for various biological processes and diseases. However, most existing computational methods for identifying PPI modulators require either target structure or reference modulators, which restricts their applicability to novel PPI targets. To address this challenge, we propose MultiPPIMI, a sequence-based deep learning framework that predicts the interaction between any given PPI target and modulator. MultiPPIMI integrates multimodal representations of PPI targets and modulators and uses a bilinear attention network to capture intermolecular interactions. Experimental results on our curated benchmark data set show that MultiPPIMI achieves an average AUROC of 0.837 in three cold-start scenarios and an AUROC of 0.994 in the random-split scenario. Furthermore, the case study shows that MultiPPIMI can assist molecular docking simulations in screening inhibitors of Keap1/Nrf2 PPI interactions. We believe that the proposed method provides a promising way to screen PPI-targeted modulators.

Natural products modulate cell apoptosis: a promising way for treating endometrial cancer

Endometrial cancer (EC) is a prevalent epithelial malignancy in the uterine corpus's endometrium and myometrium. Regulating apoptosis of endometrial cancer cells has been a promising approach for treating EC. Recent in-vitro and in-vivo studies show that numerous extracts and monomers from natural products have pro-apoptotic properties in EC. Therefore, we have reviewed the current studies regarding natural products in modulating the apoptosis of EC cells and summarized their potential mechanisms. The potential signaling pathways include the mitochondria-dependent apoptotic pathway, endoplasmic reticulum stress (ERS) mediated apoptotic pathway, the mitogen-activated protein kinase (MAPK) mediated apoptotic pathway, NF-κB-mediated apoptotic pathway, PI3K/AKT/mTOR mediated apoptotic pathway, the p21-mediated apoptotic pathway, and other reported pathways. This review focuses on the importance of natural products in treating EC and provides a foundation for developing natural products-based anti-EC agents.

Mathematical model of the cell signaling pathway based on the extended Boolean network model with a stochastic process

BACKGROUND

In cell signaling pathways, proteins interact with each other to determine cell fate in response to either cell-extrinsic (micro-environmental) or intrinsic cues. One of the well-studied pathways, the mitogen-activated protein kinase (MAPK) signaling pathway, regulates cell processes such as differentiation, proliferation, apoptosis, and survival in response to various micro-environmental stimuli in eukaryotes. Upon micro-environmental stimulus, receptors on the cell membrane become activated. Activated receptors initiate a cascade of protein activation in the MAPK pathway. This activation involves protein binding, creating scaffold proteins, which are known to facilitate effective MAPK signaling transduction.

RESULTS

This paper presents a novel mathematical model of a cell signaling pathway coordinated by protein scaffolding. The model is based on the extended Boolean network approach with stochastic processes. Protein production or decay in a cell was modeled considering the stochastic process, whereas the protein-protein interactions were modeled based on the extended Boolean network approach. Our model fills a gap in the binary set applied to previous models. The model simultaneously considers the stochastic process directly. Using the model, we simulated a simplified mitogen-activated protein kinase (MAPK) signaling pathway upon stimulation of both a single receptor at the initial time and multiple receptors at several time points. Our simulations showed that the signal is amplified as it travels down to the pathway from the receptor, generating substantially amplified downstream ERK activity. The noise generated by the stochastic process of protein self-activity in the model was also amplified as the signaling propagated through the pathway.

CONCLUSIONS

The signaling transduction in a simplified MAPK signaling pathway could be explained by a mathematical model based on the extended Boolean network model with a stochastic process. The model simulations demonstrated signaling amplifications when it travels downstream, which was already observed in experimental settings. We also highlight the importance of stochastic activity in regulating protein inactivation.

Structural landscapes of PPI interfaces

Proteins are capable of highly specific interactions and are responsible for a wide range of functions, making them attractive in the pursuit of new therapeutic options. Previous studies focusing on overall geometry of protein-protein interfaces, however, concluded that PPI interfaces were generally flat. More recently, this idea has been challenged by their structural and thermodynamic characterisation, suggesting the existence of concave binding sites that are closer in character to traditional small-molecule binding sites, rather than exhibiting complete flatness. Here, we present a large-scale analysis of binding geometry and physicochemical properties of all protein-protein interfaces available in the Protein Data Bank. In this review, we provide a comprehensive overview of the protein-protein interface landscape, including evidence that even for overall larger, more flat interfaces that utilize discontinuous interacting regions, small and potentially druggable pockets are utilized at binding sites.

pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors

Protein-protein interactions are promising sites for development of selective drugs; however, they have generally been viewed as challenging targets. Molecules targeting protein-protein interactions tend to be larger and more lipophilic than other drug-like molecules, mimicking the properties of interacting interfaces. Here, we propose a machine learning approach that uses a graph-based representation of small molecules to guide identification of inhibitors modulating protein-protein interactions, pdCSM-PPI. This approach was applied to 21 different PPI targets. We developed interaction-specific models that were able to accurately identify active compounds achieving MCC and F1 scores up to 1, and Pearson's correlations up to 0.87, outperforming previous approaches. Using insights from these individual models, we developed a generic protein-protein interaction modulator predictive model, which accurately predicted IC50 with a Pearson's correlation of 0.64 on a low redundancy blind test. Importantly, we were able to accurately identify active from inactive compounds, achieving an AUC of 0.77 and sensitivity and specificity of 76% and 78%, respectively. We believe pdCSM-PPI will be an important tool to help guide more efficient screening of new PPI inhibitors; it is freely available as an easy-to-use web server and API at http://biosig.unimelb.edu.au/pdcsm_ppi.

Inflammatory signaling sensitizes Piezo1 mechanotransduction in articular chondrocytes as a pathogenic feed-forward mechanism in osteoarthritis

Osteoarthritis is a global health problem that affects load-bearing joints, causing loss of mobility and enormous healthcare costs. However, disease-modifying approaches are lacking. Here, we report a cellular mechanism of inflammatory signaling in chondrocytes, the cellular component of cartilage. We show how osteoarthritis-relevant levels of interleukin-1α reprogram articular chondrocytes so that they become more susceptible to mechanical trauma, which chondrocytes sense via Piezo1/2-mechanosensitive ion channels. We uncover that IL-1α enhances gene expression of Piezo1 in primary articular chondrocytes underlying Piezo1 enhanced function. We elucidate signaling from membrane to nucleus, including transcription factors that enhance Piezo1 expression. We also define consequences of increased expression of Piezo1, for mechanotransduction and at rest, that implicate this reprogramming mechanism in osteoarthritis pathogenesis.

Osteoarthritis (OA) is a painful and debilitating condition of synovial joints without any disease-modifying therapies [A. M. Valdes, T. D. Spector, Nat. Rev. Rheumatol. 7, 23–32 (2011)]. We previously identified mechanosensitive PIEZO channels, PIEZO1 and PIEZO2, both expressed in articular cartilage, to function in chondrocyte mechanotransduction in response to injury [W. Lee et al., Proc. Natl. Acad. Sci. U.S.A. 111, E5114–E5122 (2014); W. Lee, F. Guilak, W. Liedtke, Curr. Top. Membr. 79, 263–273 (2017)]. We therefore asked whether interleukin-1–mediated inflammatory signaling, as occurs in OA, influences Piezo gene expression and channel function, thus indicative of maladaptive reprogramming that can be rationally targeted. Primary porcine chondrocyte culture and human osteoarthritic cartilage tissue were studied. We found that interleukin-1α (IL-1α) up-regulated Piezo1 in porcine chondrocytes. Piezo1 expression was significantly increased in human osteoarthritic cartilage. Increased Piezo1 expression in chondrocytes resulted in a feed-forward pathomechanism whereby increased function of Piezo1 induced excess intracellular Ca²⁺ at baseline and in response to mechanical deformation. Elevated resting state Ca²⁺ in turn rarefied the F-actin cytoskeleton and amplified mechanically induced deformation microtrauma. As intracellular substrates of this OA-related inflammatory pathomechanism, in porcine articular chondrocytes exposed to IL-1α, we discovered that enhanced Piezo1 expression depended on p38 MAP-kinase and transcription factors HNF4 and ATF2/CREBP1. CREBP1 directly bound to the proximal PIEZO1 gene promoter. Taken together, these signaling and genetic reprogramming events represent a detrimental Ca²⁺-driven feed-forward mechanism that can be rationally targeted to stem the progression of OA.

Polyphenol-Enriched Extracts from Trapa acornis Husks Inhibit Her2-Positive SK-BR-3 Breast Cancer Cell Proliferation and In Vivo Tumor Angiogenesis

The study aimed to investigate the antitumor effects of Trapa acornis husks (TAH) extract on SK-BR-3 cells of Her2-positive breast cancer. The bioactive compounds of TAH extracts were analyzed qualitatively and quantitatively by Ultra-Performance Liquid Chromatography/Mass Spectrometry (UPLC-MS)/high-performance liquid chromatographic system (HPLC). The effects of TAH extracts on cell proliferation, cell cycle, and apoptosis of SK-BR-3 cells were determined by CCK-8 and flow cytometry. Besides, the In Vivo antitumor effect of TAH extracts was detected. UPLC-MS/HPLC showed that the main bioactive compounds of TAH were gallic acid and galloylglucose derivatives. TAH extracts significantly inhibited the proliferation of SK-BR-3 cells in a dose- and time-dependent manner (P < 0.01). With the increase of TAH extracts concentration, cells in G2/M stage were increased and cell apoptosis was significantly increased. Immunohistochemical analysis showed that TAH extracts can significantly reduce the positive expression rate of Ki67 and Factor VIII index in tumor tissues. The mRNA expression levels of VEGF, MMP2, MMP9, and uPA were reduced after TAH extracts intervention (P < 0.01). TAH extracts also decreased the protein expression of p-Her2, p-ERK1/2, VEGF, MMP2, MMP9, and uPA (P < 0.01). In conclusion, polyphenol-enriched extracts from TAH might inhibit breast cancer cell proliferation and In Vivo tumor angiogenesis.

Molecular cloning and characterization of a cDNA encoding extracellular signal-regulated kinase (ERK) from the blood clam Tegillarca granosa

The blood clam Tegillarca granosa is a member of the most economically important bivalve mollusk species in the Asia-Pacific region. T. granosa entirely depends on innate immunity for pathogen defense. However, there are very few reports on the immune responses of T. granosa to various pathogens. In our study, we cloned and characterized an ERK homolog from T. granosa, which was defined as TgERK. The full-length cDNA sequence of TgERK was 1644 bp in length and encoded a conserved S_TKc domain (residues 21-309) in the N terminus. The TgERK mRNA was universally expressed in all examined tissues, with the highest expression level found in hemocytes. Lipopolysaccharide (LPS) and Vibrio alginolyticus challenges strongly enhanced the expression of ERK in T. granosa, which was consistent with the results of an in vitro challenge study with cultured T. granosa hemocytes. Pathogen invasion also upregulated the expression of downstream genes in the ERK signaling pathway, such as CREB, c-Fos and SIRT1. Moreover, TgERK knockdown resulted in decreased expression of these downstream genes. Inhibition of ERK by its inhibitor U0126 decreased T. granosa hemocyte viability in a dose-dependent manner. Taken together, our results demonstrated that TgERK was a crucial regulator of the immune response to pathogen invasion, which indicated new knowledge of hemocyte immunity in T. granosa and provided a novel key molecule in immune regulation for controlling diseases in T. granosa aquaculture.

ERK/MAPK signalling pathway and tumorigenesis

Mitogen-activated protein kinase (MAPK) cascades are key signalling pathways that regulate a wide variety of cellular processes, including proliferation, differentiation, apoptosis and stress responses. The MAPK pathway includes three main kinases, MAPK kinase kinase, MAPK kinase and MAPK, which activate and phosphorylate downstream proteins. The extracellular signal-regulated kinases ERK1 and ERK2 are evolutionarily conserved, ubiquitous serine-threonine kinases that regulate cellular signalling under both normal and pathological conditions. ERK expression is critical for development and their hyperactivation plays a major role in cancer development and progression. The Ras/Raf/MAPK (MEK)/ERK pathway is the most important signalling cascade among all MAPK signal transduction pathways, and plays a crucial role in the survival and development of tumour cells. The present review discusses recent studies on Ras and ERK pathway members. With respect to processes downstream of ERK activation, the role of ERK in tumour proliferation, invasion and metastasis is highlighted, and the role of the ERK/MAPK signalling pathway in tumour extracellular matrix degradation and tumour angiogenesis is emphasised.

mCSM-PPI2: predicting the effects of mutations on protein-protein interactions

Protein-protein Interactions are involved in most fundamental biological processes, with disease causing mutations enriched at their interfaces. Here we present mCSM-PPI2, a novel machine learning computational tool designed to more accurately predict the effects of missense mutations on protein-protein interaction binding affinity. mCSM-PPI2 uses graph-based structural signatures to model effects of variations on the inter-residue interaction network, evolutionary information, complex network metrics and energetic terms to generate an optimised predictor. We demonstrate that our method outperforms previous methods, ranking first among 26 others on CAPRI blind tests. mCSM-PPI2 is freely available as a user friendly webserver at http://biosig.unimelb.edu.au/mcsm_ppi2/.

Nuclear ERK: Mechanism of Translocation, Substrates, and Role in Cancer

The extracellular signal-regulated kinases 1/2 (ERK) are central signaling components that regulate stimulated cellular processes such as proliferation and differentiation. When dysregulated, these kinases participate in the induction and maintenance of various pathologies, primarily cancer. While ERK is localized in the cytoplasm of resting cells, many of its substrates are nuclear, and indeed, extracellular stimulation induces a rapid and robust nuclear translocation of ERK. Similarly to other signaling components that shuttle to the nucleus upon stimulation, ERK does not use the canonical importinα/β mechanism of nuclear translocation. Rather, it has its own unique nuclear translocation signal (NTS) that interacts with importin7 to allow stimulated shuttling via the nuclear pores. Prevention of the nuclear translocation inhibits proliferation of B-Raf- and N/K-Ras-transformed cancers. This effect is distinct from the one achieved by catalytic Raf and MEK inhibitors used clinically, as cells treated with the translocation inhibitors develop resistance much more slowly. In this review, we describe the mechanism of ERK translocation, present all its nuclear substrates, discuss its role in cancer and compare its translocation to the translocation of other signaling components. We also present proof of principle data for the use of nuclear ERK translocation as an anti-cancer target. It is likely that the prevention of nuclear ERK translocation will eventually serve as a way to combat Ras and Raf transformed cancers with less side-effects than the currently used drugs.

The nuclear translocation of the kinases p38 and JNK promotes inflammation-induced cancer

The stimulated nuclear translocation of signaling proteins, such as MAPKs, is a necessity for the initiation and regulation of their physiological functions. Previously, we determined that nuclear translocation of the MAPKs p38 and JNK involves binding to heterodimers comprising importin 3 and either importin 7 or importin 9. Here, we identified the importin-binding region in p38 and JNK and developed a myristoylated peptide targeting this site that we called PERY. The PERY peptide specifically blocked the interaction of p38 and JNK with the importins, restricted their nuclear translocation, and inhibited phosphorylation of their nuclear (but not cytoplasmic) substrates. Through these effects, the PERY peptide reduced the proliferation of several (but not all) cancer cell lines in culture and inhibited the growth of a human breast cancer xenograft in mice. In addition, the PERY peptide substantially inhibited inflammation in mice, as manifested in models of colitis and colitis-associated colon cancer. The PERY peptide more effectively prevented colon cancer development than did a commercial p38 inhibitor. In vivo analysis further suggested that this effect was mediated by PERY peptide-induced prevention of the nuclear translocation of p38 in macrophages. Together, these results support the use of the nuclear translocation of p38 and JNK as a novel drug target to treat various cancers and inflammation-induced diseases.

c-Jun N-terminal kinase and p38 mitogen-activated protein kinase pathways link capacitation with apoptosis and seminal plasma proteins protect sperm by interfering with both routes†

The mitogen-activated protein kinase (MAPK), c-Jun N-terminal kinase (JNK), and p38 MAP kinase (p38) signaling cascades are involved in triggering apoptosis in somatic cells. Given that spermatozoa are able to undergo apoptosis, we tested the hypothesis that these pathways might be functional in ram spermatozoa as two signal transduction mechanisms that contribute to the modulation of capacitation and apoptosis. Indirect immunofluorescence and western blot analysis evidenced the presence of JNK and p38 in ram spermatozoa. To verify the involvement of these enzymes in sperm physiology, we determined the effect of specific inhibitors of JNK or p38 on in vitro capacitation induced with either cAMP-elevating agents or epidermal growth factor (EGF). Both inhibitions reduced the EGF-induced capacitation with a decrease in the chlortetracycline capacitated-sperm pattern, protein tyrosine phosphorylation, phosphatidylserine externalization, caspase-3 and -7 activation, and the proportion of DNA-damaged spermatozoa. No significant changes were found in the high-cAMP capacitated samples. The addition of 3.4 mg/ml seminal plasma proteins (SPPs) to the EGF-containing samples, either alone or together with each inhibitor, resulted in a decreased proportion of capacitated sperm pattern, protein tyrosine phosphorylation, loss of plasma membrane integrity, and apoptotic alterations. Furthermore, SPPs significantly reduced the phosphorylation level of JNK and p38 MAPK (active forms). These findings show a relationship between capacitation and apoptosis, and represent a step forward in the knowledge of the SPP protective mechanism in spermatozoa.

Macrophage migration inhibitory factor activates inflammatory responses of astrocytes through interaction with CD74 receptor

Astrocytes, the major glial cell population of the central nervous system (CNS), play important physiological roles related to CNS homeostasis. Growing evidence demonstrates that astrocytes trigger innate immune responses under challenge of a variety of proinflammatory cytokines. Macrophage migration inhibitory factor (MIF), a proinflammatory cytokine mainly secreted from monocytes/macrophages, is involved in inflammation-associated pathophysiology. Here, we displayed that expression of MIF significantly increased following spinal cord injury, in colocalization with microglia and astrocytes. MIF elicited inflammatory responses of astrocytes via activation of CD74 receptor and extracellular signal-related kinase (ERK) pathway. Transcriptome analysis revealed that inflammation-related factors cholesterol 25-hydroxylase (Ch25h) and phospholipase A2-IIA (Pla2g2a), downstream of MIF/CD74 axis, were potentially implicated in the mediating inflammatory response of astrocytes. Our results provided a new target for interference of CNS inflammation after insults.

Activation of the ERK1/2-MAPK Signaling Pathway by Complement Serum in UV-POS-Pretreated ARPE-19 Cells

BACKGROUND

Retinal pigment epithelial (RPE) cells undergo functional changes upon complement stimulation, which play a role in the pathogenesis of age-related macular degeneration (AMD). These effects are in part enhanced by pretreating ARPE-19 cells with UV-irradiated photoreceptor outer segments (UV-POS) in vitro. The aim of this study was to investigate the effects of human complement serum (HCS) treatment on p44/42 mitogen-activated protein kinase (extracellular signal-regulated kinase 1/2 [ERK1/2]) activation in ARPE-19 cells pretreated with UV-POS.

METHODS

UV-POS-pretreated ARPE-19 cells were stimulated with 5% HCS or heat-inactivated HCS (HI-HCS) as a control. Pro tein expression of phosphorylated (activated) ERK1/2, total ERK1/2, Bax, and Bcl-2 was analyzed by Western blotting. Cell culture supernatants were analyzed for IL-6, IL-8, MCP-1, and VEGF by enzyme-linked immunosorbent assay (ELISA). Furthermore, extra- and intracellular reactive oxygen species (ROS) were determined.

RESULTS

The amount of phosphorylated ERK1/2 was increased in UV-POS-pretreated ARPE-19 cells, especially in combination with HCS stimulation, compared to non-pretreated ARPE-19 cells incubated with HCS alone or HI-HCS. The same observation was made for Bax and Bcl-2 expression. Furthermore, an increase in extra- and intracellular ROS was detected in UV-POS-pretreated ARPE-19 cells. The ELISA data showed that the production of IL-6, IL-8, and MCP-1 tended to increase in response to HCS in both UV-POS-pretreated and non-pretreated ARPE-19 cells.

CONCLUSIONS

Our data imply that ERK1/2 activation in ARPE-19 cells may represent a response mechanism to cellular and oxidative stress, associated with apoptosis-regulating factors such as Bax and Bcl-2, which might play a role in AMD, while ERK1/2 seems not to represent the crucial signaling pathway mediating the functional changes in RPE cells in response to complement stimulation.

The Nuclear Translocation of ERK

The ERK1 and ERK2 (ERK1/2) cascade is a central signaling pathway activated by a wide variety of extracellular agents that transmit the messages of G Protein Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Being such a central pathway, the activity of the cascade is well regulated, including by dynamic changes of the subcellular localization of components of the ERK1/2 cascade. In resting cells, ERK1/2 are localized in the cytosol due to their interactions with different anchoring proteins. After stimulation, ERK1/2 are phosphorylated by MEK1/2 on their regulatory TEY motif, which permits their detachment from the anchoring proteins. This detachment exposes ERK1/2 to additional phosphorylation on two serine residues (SPS motif) within the nuclear translocation signal (NTS) of the kinases. This additional phosphorylation allows ERK1/2 to interact with importin7, which consequently promotes their translocation to the nucleus. More studies are still required in order to better understand the mechanism and consequence of the nuclear translocation of ERK1/2. In this chapter, we describe some of the techniques used to study nuclear translocation of ERK1/2 in mammalian cells. We briefly mention methods such as digitonin permeabilization and cellular fractionation, as well as overexpression of reporter constructs. More thoroughly, we describe immunofluorescence, immunoprecipitation, and proximity ligation assay (PLA) approaches that are routinely used in our laboratory. Hopefully, the increase of knowledge based on these methods will open more opportunities for the identification of new therapeutic targets for diseases where the ERK1/2 cascade is dysregulated, such as cancer, neurodegenerative diseases, and diabetes.

Alterations of the nuclear transport system in hepatocellular carcinoma - New basis for therapeutic strategies

Hepatocellular carcinoma (HCC) is among the most prevalent human malignancies worldwide with rising incidence in industrialised countries, few therapeutic options and poor prognosis. To expand and improve therapeutic strategies, identification of drug targets involved in several liver cancer-related pathways is crucial. Virtually all signal transduction cascades cross the nuclear envelope and therefore require components of the nuclear transport system (NTS), including nuclear transport receptors (e.g. importins and exportins) and the nuclear pore complex. Accordingly, members of the NTS represent promising targets for therapeutic intervention. Selective inhibitors of nuclear export have already entered clinical trials for various malignancies. Herein, we review the current knowledge regarding alterations of the NTS and their potential for targeted therapy in HCC.

Endogenous, regulatory cysteine sulfenylation of ERK kinases in response to proliferative signals

ERK-dependent signaling is key to many pathways through which extracellular signals are transduced into cell-fate decisions. One conundrum is the way in which disparate signals induce specific responses through a common, ERK-dependent kinase cascade. While studies have revealed intricate ways of controlling ERK signaling through spatiotemporal localization and phosphorylation dynamics, additional modes of ERK regulation undoubtedly remain to be discovered. We hypothesized that fine-tuning of ERK signaling could occur by cysteine oxidation. We report that ERK is actively and directly oxidized by signal-generated H₂O₂ during proliferative signaling, and that ERK oxidation occurs downstream of a variety of receptor classes tested in four cell lines. Furthermore, within the tested cell lines and proliferative signals, we observed that both activation loop-phosphorylated and non-phosphorylated ERK undergo sulfenylation in cells and that dynamics of ERK sulfenylation is dependent on the cell growth conditions prior to stimulation. We also tested the effect of endogenous ERK oxidation on kinase activity and report that phosphotransfer reactions are reversibly inhibited by oxidation by as much as 80-90%, underscoring the importance of considering this additional modification when assessing ERK activation in response to extracellular signals.

A cellular threshold for active ERK1/2 levels determines Raf/MEK/ERK-mediated growth arrest versus death responses

In addition to its conventional role for cell proliferation and survival, the Raf/MEK/Extracellular signal-regulated kinase (ERK) pathway can also induce growth arrest and death responses, if aberrantly activated. Here, we determined a molecular basis of ERK1/2 signaling that underlies these growth inhibitory physiological outputs. We found that overexpression of ERK1 or ERK2 switches ΔRaf-1:ER-induced growth arrest responses to caspase-dependent apoptotic death responses in different cell types. These death responses, however, were reverted to growth arrest responses upon titration of cellular phospho-ERK1/2 levels by the MEK1/2 inhibitor AZD6244. These data suggest that a cellular threshold for active ERK1/2 levels exists and affects the cell fate between death and growth arrest. We also found that death-mediating ability of ERK2 is abolished by the catalytic site-disabling Lys52Arg replacement or significantly attenuated by the F-site recruitment site-disabling Tyr261Asn replacement, although unaffected by the mutations that disable the common docking groove or the dimerization interface. Therefore, ERK1/2 mediates death signaling dependently of kinase activity and specific physical interactions. Intriguingly, Tyr261Asn-replaced ERK2 could still mediate growth arrest signaling, further contrasting the molecular basis of ERK1/2-mediated growth arrest and death signaling. These data reveal a mechanism underlying the role of ERK1/2 as a focal point of Raf/MEK/ERK-mediated growth arrest and death signaling.

The Role of ERK Signaling in Experimental Autoimmune Encephalomyelitis

Extracellular signal-regulated kinase (ERK) signaling plays a crucial role in regulating immune cell function and has been implicated in autoimmune disorders. To date, all commercially available inhibitors of ERK target upstream components, such as mitogen-activated protein (MAP) kinase/ERK kinase (MEKs), but not ERK itself. Here, we directly inhibit nuclear ERK translocation by a novel pharmacological approach (Glu-Pro-Glu (EPE) peptide), leading to an increase in cytosolic ERK phosphorylation during T helper (Th)17 cell differentiation. This was accompanied by diminished secretion of granulocyte-macrophage colony-stimulating factor (GM-CSF), a cytokine influencing the encephalitogenicity of Th17 cells. Neither the production of the cytokine interleukin (IL)-17 nor the proliferation rate of T cells was affected by the EPE peptide. The in vivo effects of ERK inhibition were challenged in two independent variants of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). Overall, ERK inhibition had only a very minor impact on the clinical disease course of EAE. This indicates that while ERK translocation might promote encephalitogenicity in T cells in vitro by facilitating GM-CSF production, this effect is overcome in more complex in vivo animal models of central nervous system (CNS) autoimmunity.

Stress-induced nuclear translocation of CDK5 suppresses neuronal death by downregulating ERK activation via VRK3 phosphorylation

Although extracellular signal-related kinase 1/2 (ERK 1/2) activity is generally associated with cell survival, prolonged ERK activation induced by oxidative stress also mediates neuronal cell death. Here we report that oxidative stress-induced cyclin-dependent kinase 5 (CDK5) activation stimulates neuroprotective signaling via phosphorylation of vaccinia-related kinase 3 (VRK3) at Ser 108. The binding of vaccinia H1-related (VHR) phosphatase to phosphorylated VRK3 increased its affinity for phospho-ERK and subsequently downregulated ERK activation. Overexpression of VRK3 protected human neuroblastoma SH-SY5Y cells against hydrogen peroxide (H₂O₂)-induced apoptosis. However the CDK5 was unable to phosphorylate mutant VRK3, and thus the mutant forms of VRK3 could not attenuate apoptotic process. Suppression of CDK5 activity results in increase of ERK activation and elevation of proapoptotic protein Bak expression in mouse cortical neurons. Results from VRK3-deficient neurons were further confirmed the role of VRK3 phosphorylation in H₂O₂-evoked ERK regulation. Importantly, we showed an association between phospho-VRK3 levels and the progression of human Alzheimer’s disease (AD) and Parkinson’s disease (PD). Together our work reveals endogenous protective mechanism against oxidative stress-induced neuronal cell death and suggest VRK3 as a potential therapeutic target in neurodegenerative diseases.

C-terminal Src Kinase Gates Homeostatic Synaptic Plasticity and Regulates Fasciclin II Expression at the Drosophila Neuromuscular Junction

Forms of homeostatic plasticity stabilize neuronal outputs and promote physiologically favorable synapse function. A well-studied homeostatic system operates at the Drosophila melanogaster larval neuromuscular junction (NMJ). At the NMJ, impairment of postsynaptic glutamate receptor activity is offset by a compensatory increase in presynaptic neurotransmitter release. We aim to elucidate how this process operates on a molecular level and is preserved throughout development. In this study, we identified a tyrosine kinase-driven signaling system that sustains homeostatic control of NMJ function. We identified C-terminal Src Kinase (Csk) as a potential regulator of synaptic homeostasis through an RNAi- and electrophysiology-based genetic screen. We found that Csk loss-of-function mutations impaired the sustained expression of homeostatic plasticity at the NMJ, without drastically altering synapse growth or baseline neurotransmission. Muscle-specific overexpression of Src Family Kinase (SFK) substrates that are negatively regulated by Csk also impaired NMJ homeostasis. Surprisingly, we found that transgenic Csk-YFP can support homeostatic plasticity at the NMJ when expressed either in the muscle or in the nerve. However, only muscle-expressed Csk-YFP was able to localize to NMJ structures. By immunostaining, we found that Csk mutant NMJs had dysregulated expression of the Neural Cell Adhesion Molecule homolog Fasciclin II (FasII). By immunoblotting, we found that levels of a specific isoform of FasII were decreased in homeostatically challenged GluRIIA mutant animals–but markedly increased in Csk mutant animals. Additionally, we found that postsynaptic overexpression of FasII from its endogenous locus was sufficient to impair synaptic homeostasis, and genetically reducing FasII levels in Csk mutants fully restored synaptic homeostasis. Based on these data, we propose that Csk and its SFK substrates impinge upon homeostatic control of NMJ function by regulating downstream expression or localization of FasII.

Homeostasis is a fundamental topic in biology. Individual cells and systems of cells constantly monitor their environments and adjust their outputs in order to maintain physiological properties within ranges that can support life. The nervous system is no exception. Synapses and circuits are endowed with a capacity to respond to environmental challenges in a homeostatic fashion. As a result, synaptic output stays within an appropriate physiological range. We know that homeostasis is a fundamental form of regulation in animal nervous systems, but we have very little information about how it works. In this study, we examine the fruit fly Drosophila melanogaster and its ability to maintain normal levels of synaptic output over long periods of developmental time. We identify new roles in this process for classical signaling molecules called C-terminal Src kinase, Src family kinases, as well as a neuronal cell adhesion molecule called Fasciclin II, which was previously shown to stabilize synaptic contacts between neurons and muscles. Our work contributes to a broader understanding of how neurons work to maintain stable outputs. Ultimately, this type of knowledge could have important implications for neurological disorders in which stability is lost, such as forms of epilepsy or ataxia.

The dynamic subcellular localization of ERK: mechanisms of translocation and role in various organelles

The dynamic subcellular localization of ERK in resting and stimulated cells plays an important role in its regulation. In resting cells, ERK localizes in the cytoplasm, and upon stimulation, it translocates to its target substrates and organelles. ERK signaling initiated from different places in resting cells has distinct outcomes. In this review, we summarize the mechanisms of ERK1/2 translocation to the nucleus and mitochondria, and of ERK1c to the Golgi. We also show that ERK1/2 translocation to the nucleus is a useful anti cancer target. Unraveling the complex subcellular localization of ERK and its dynamic changes upon stimulation provides a better understanding of the regulation of ERK signaling and may result in the development of new strategies to combat ERK-related diseases.

The ERK cascade inhibitors: Towards overcoming resistance

The RAS-ERK pathway plays a major regulatory role in various cellular processes. This pathway is hyperactivated and takes an active part in the malignant transformation of more than 85% of cancers. The hyperactivation is mainly due to oncogenic activating mutations in the pathway's components RAS, RAF and MEK, but also due to indirect mechanisms in cells transformed by other oncogenes. Various inhibitors targeting the different tiers of the cascade have been successfully developed and clinically approved, while some are still undergoing preclinical and clinical evaluation. Treatments with the clinically approved RAF and MEK inhibitors have substantially improved the clinical outcome of metastatic mutated-BRAF melanoma. However, the rapid emergence of drug resistance of initially responsive cancers and limited efficacy towards other cancers has led to only marginal patient benefit. Deciphering the molecular mechanisms underlying intrinsic or acquired resistance is a necessity in order to enhance the treatment efficacy of ERK-addicted cancers. Therefore, many studies in the past 5 years embarked on this campaign, revealing several resistance mechanisms. These include, expression of drug-resistant RAF isoforms, molecular or genetic alterations of active downstream components, overexpression of upstream components of the cascade that can reactivate ERK and other survival-related pathways. The understanding of these molecular resistance mechanisms led to further development of drugs that can overcome drug resistance, including our own effort aiming to prevent the nuclear translocation of ERK without affecting its activation. In this review we will focus on the mechanisms underlying drug resistance and efforts to develop activity-independent, more efficacious, antitumor drugs.

Role of PI4K and PI3K-AKT in ERK1/2 activation by GnRH in the pituitary gonadotropes

The role of PI4K and PI3K-AKT in ERK1/2 activation by GnRH was examined. A relatively long preincubation (60 min) with wortmannin (10 nM and 10 μM), and LY294002 (10 μM and 100 μM) (doses known to inhibit PI3K and PI4K, respectively), were required to inhibit GnRH-and PMA-stimulated ERK1/2 activity in αT3-1 and LβT2 gonadotrope cells. A similar preincubation protocol was required to demonstrate inhibition of IGF-1-stimulated AKT activation lending support for the need of prolonged incubation (60 min) with wortmannin in contrast to other cellular systems. To rule out that the inhibitors acted upon PI(4,5)P2 levels, we followed the [Ca(2+)]i response to GnRH and found that wortmannin has no significant effect on GnRH-induced [Ca(2+)]i responses. Surprisingly, GnRH and PMA reduced, while IGF-1 increased AKT phosphorylation. We suggest that PI3K inhibits GnRH-stimulated αGSU activity, has no effect upon GnRH-stimulated LHβ activity and enhanced the GnRH-stimulated FSHβ transcription. Hence, PI4K and PI3K-AKT play a role in GnRH to ERK1/2 signaling, while PI3K may regulate also GnRH-induced gonadotropin gene expression.

The nuclear translocation of ERK1/2 as an anticancer target

A hallmark of the ERK1/2 functioning is their nuclear translocation, which is mainly required for the induction of proliferation. Activated ERK1/2 molecules that remain in the cytoplasm initiate other activities, including immediate feedback loops. Prevention of the nuclear translocation should therefore inhibit proliferation, without affecting cytoplasm-induced cellular processes. Here we present an NTS-derived myristoylated phosphomimetic peptide, which blocks the interaction of importin7 and ERK1/2, and consequently the nuclear translocation of the latter. In culture, the peptide induces apoptosis of melanoma cells inhibits the viability of other cancer cells, but has no effect on non-transformed, immortalized cells. It even inhibits the viability of PLX4032- and U0126-resistant melanoma cells. In xenograft models, the peptide inhibits several cancers, and acts much better than PLX4032 in preventing melanoma recurrence. This study provides a proof of concept for using the nuclear translocation of ERK1/2 as a drug target for the combat of various ERK1/2-related cancers.

Inhibition of host extracellular signal-regulated kinase (ERK) activation decreases new world alphavirus multiplication in infected cells

New World alphaviruses belonging to the family Togaviridae are classified as emerging infectious agents and Category B select agents. Our study is focused on the role of the host extracellular signal-regulated kinase (ERK) in the infectious process of New World alphaviruses. Infection of human cells by Venezuelan equine encephalitis virus (VEEV) results in the activation of the ERK-signaling cascade. Inhibition of ERK1/2 by the small molecule inhibitor Ag-126 results in inhibition of viral multiplication. Ag-126-mediated inhibition of VEEV was due to potential effects on early and late stages of the infectious process. While expression of viral proteins was down-regulated in Ag-126 treated cells, we did not observe any influence of Ag-126 on the nuclear distribution of capsid. Finally, Ag-126 exerted a broad-spectrum inhibitory effect on New World alphavirus multiplication, thus indicating that the host kinase, ERK, is a broad-spectrum candidate for development of novel therapeutics against New World alphaviruses.

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VEEV infection activated multiple components of the ERK signaling cascade.

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Inhibition of ERK activation using Ag-126 inhibited VEEV multiplication.

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Activation of ERK by Ceramide C6 increased infectious titers of TC-83.

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Ag-126 inhibited virulent strains of all New World alphaviruses.

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Ag-126 treatment increased percent survival of infected cells.

Tay bridge is a negative regulator of EGFR signalling and interacts with Erk and Mkp3 in the Drosophila melanogaster wing

The regulation of Extracellular regulated kinase (Erk) activity is a key aspect of signalling by pathways activated by extracellular ligands acting through tyrosine kinase transmembrane receptors. In this process, participate proteins with kinase activity that phosphorylate and activate Erk, as well as different phosphatases that inactivate Erk by de-phosphorylation. The state of Erk phosphorylation affects not only its activity, but also its subcellular localization, defining the repertoire of Erk target proteins, and consequently, the cellular response to Erk. In this work, we characterise Tay bridge as a novel component of the EGFR/Erk signalling pathway. Tay bridge is a large nuclear protein with a domain of homology with human AUTS2, and was previously identified due to the neuronal phenotypes displayed by loss-of-function mutations. We show that Tay bridge antagonizes EGFR signalling in the Drosophila melanogaster wing disc and other tissues, and that the protein interacts with both Erk and Mkp3. We suggest that Tay bridge constitutes a novel element involved in the regulation of Erk activity, acting as a nuclear docking for Erk that retains this protein in an inactive form in the nucleus.

Extracellular regulated kinases (Erk) mediate signalling by pathways activated by tyrosine kinase transmembrane receptors. The level of activated Erk depends on a highly regulated balance between cytoplasmic kinases and nuclear/cytoplasmic phosphatases, which determine the state of Erk phosphorylation. This affects Erk activity and its subcellular localization, defining the repertoire of Erk targets, and consequently, the cellular response to Erk. In this work, we use a genetic approach to characterise the gene tay bridge as a novel component of the EGFR/Erk signalling pathway. Tay bridge has a domain of homology with human AUTS2, and was previously identified due to the neuronal phenotypes displayed by loss-of-function mutations. We show that Tay bridge antagonizes EGFR signalling in the Drosophila melanogaster wing disc and other tissues, and that the protein interacts with both Erk and Mkp3. We suggest that Tay bridge constitutes a novel element involved in the regulation of Erk activity, acting as a nuclear docking for Erk that retains this protein in an inactive form in the nucleus. These results could provide important insights into the clinical consequences of AUTS2 mutations in humans, which are related to behavioural perturbations including autism, mental retardation, Attention Deficit Hyperactivity Disorder and alcohol drinking behaviour.

Stimulated nuclear import by β-like importins

Classic nuclear shuttling is mediated by an importin-α∙β heterodimer that binds to cargoes containing a nuclear localization signal, and shuttles most nuclear proteins immediately after their translation. Aside from this canonical mechanism, kariopheryn-βs or β-like importins operate by binding to non-canonical nuclear localization signals to mediate translocation without the assistance of importin-α. The mechanism by which these components operate is much less understood and is currently under investigation. Recently, several β-like importins have been implicated in the stimulated nuclear translocation of signaling proteins. Here, we propose that this group of importins might be responsible for the swift nuclear shuttling of many proteins following various stimuli.

Thrombospondin-1 mediates oncogenic Ras-induced senescence in premalignant lung tumors

Progression of premalignant lesions is restrained by oncogene-induced senescence. Oncogenic Ras triggers senescence in many organs, including the lung, which exhibits high levels of the angiogenesis inhibitor thrombospondin-1 (TSP-1). The contribution of TSP-1 upregulation to the modulation of tumorigenesis in the lung is unclear. Using a mouse model of lung cancer, we have shown that TSP-1 plays a critical and cell-autonomous role in suppressing Kras-induced lung tumorigenesis independent of its antiangiogenic function. Overall survival was decreased in a Kras-driven mouse model of lung cancer on a Tsp-1-/- background. We found that oncogenic Kras-induced TSP-1 upregulation in a p53-dependent manner. TSP-1 functioned in a positive feedback loop to stabilize p53 by interacting directly with activated ERK. TSP-1 tethering of ERK in the cytoplasm promoted a level of MAPK signaling that was sufficient to sustain p53 expression and a senescence response. Our data identify TSP-1 as a p53 target that contributes to maintaining Ras-induced senescence in the lung.

Tyrosine phosphorylation of CD13 regulates inflammatory cell-cell adhesion and monocyte trafficking

CD13 is a large cell surface peptidase expressed on the monocytes and activated endothelial cells that is important for homing to and resolving the damaged tissue at sites of injury. We showed previously that cross-linking of human monocytic CD13 with activating Abs induces strong adhesion to endothelial cells in a tyrosine kinase- and microtubule-dependent manner. In the current study, we examined the molecular mechanisms underlying these observations in vitro and in vivo. We found that cross-linking of CD13 on U937 monocytic cells induced phosphorylation of a number of proteins, including Src, FAK, and ERK, and inhibition of these abrogated CD13-dependent adhesion. We found that CD13 itself was phosphorylated in a Src-dependent manner, which was an unexpected finding because its 7-aa cytoplasmic tail was assumed to be inert. Furthermore, CD13 was constitutively associated with the scaffolding protein IQGAP1, and CD13 cross-linking induced complex formation with the actin-binding protein α-actinin, linking membrane-bound CD13 to the cytoskeleton, further supporting CD13 as an inflammatory adhesion molecule. Mechanistically, mutation of the conserved CD13 cytoplasmic tyrosine to phenylalanine abrogated adhesion; Src, FAK, and ERK phosphorylation; and cytoskeletal alterations upon Ab cross-linking. Finally, CD13 was phosphorylated in isolated murine inflammatory peritoneal exudate cells, and adoptive transfer of monocytic cell lines engineered to express the mutant CD13 were severely impaired in their ability to migrate into the inflamed peritoneum, confirming that CD13 phosphorylation is relevant to inflammatory cell trafficking in vivo. Therefore, this study identifies CD13 as a novel, direct activator of intracellular signaling pathways in pathophysiological conditions.

REV, A BRET-Based Sensor of ERK Activity

Networks of signaling molecules are activated in response to environmental changes. How are these signaling networks dynamically integrated in space and time to process particular information? To tackle this issue, biosensors of single signaling pathways have been engineered. Bioluminescence resonance energy transfer (BRET)-based biosensors have proven to be particularly efficient in that matter due to the high sensitivity of this technology to monitor protein-protein interactions or conformational changes in living cells. Extracellular signal-regulated kinases (ERK) are ubiquitously expressed and involved in many diverse cellular functions that might be encoded by the strength and spatio-temporal pattern of ERK activation. We developed a BRET-based sensor of ERK activity, called Rluc8-ERKsubstrate-Venus (REV). As expected, BRET changes of REV were correlated with ERK phosphorylation, which is required for its kinase activity. In neurons, the nature of the stimuli determines the strength, the location, or the moment of ERK activation, thus highlighting how acute modulation of ERK may encode the nature of initial stimulus to specify the consequences of this activation. This study provides evidence for suitability of REV as a new biosensor to address biological questions.

Mechanisms of MPP⁺-induced PC12 cell apoptosis via reactive oxygen species

Apoptosis of dopaminergic neurons in the nigrostriatal projection plays a crucial role in the pathogenesis of Parkinson's disease (PD). Although the detailed mechanisms responsible for dopaminergic neuron loss are still under investigation, oxidative stress is identified as a major contributor for neuronal apoptosis. In the current study, we studied the effects of MPP(+), a substrate that mimics oxidative stress, on neuron-like PC12 cells and the underlying mechanisms. PC12 cells were cultured and treated by 100 μmol/L MPP(+) for 4, 8, 16, 24 and 48 h, respectively. For drug pretreatment, the PC12 cells were incubated with N-acetyl-l-cysteine (NAC, 5 mmol/L), an antioxidant, SP600125 (20 μmol/L) or PD98059 (100 μmol/L), two pharmacological inhibitors of JNK and ERK1/2, for 1 h before addition of MPP(+). Cell apoptosis was measured by flow cytometry. The mRNA expression of Cu(2+)/Zn(2+)-SOD, GSH-Px, Bcl-2 and Bax was detected by RT-PCR. The protein expression of p-ERK1/2 and p-JNK was determined by Western blotting. Our results showed that MPP(+) exposure could induce substantial PC12 cell apoptosis. The pretreatment of SP600125 or PD98059 could effectively reduce the apoptosis rate by reducing the ratio of Bax/Bcl-2 mRNA levels. MPP(+) exposure also induced high level of reactive oxygen species (ROS), marked by dramatic increase of Cu(2+)/Zn(2+)-SOD and GSH-Px mRNA levels. The elevated ROS was strongly associated with the activation of JNK and ERK1/2 signal pathways after MPP(+) exposure, since the pretreatment of NAC significantly reduced the upregulation of p-JNK and p-ERK1/2. Finally, the pretreatment of SP600125, but not PD98059, alleviated the increase of Cu(2+)/Zn(2+)-SOD and GSH-Px mRNAs induced by MPP(+), suggesting that the activation of the JNK signal pathway, but not the ERK1/2 signal pathway, could, in some degree, antagonize the generation of ROS induced by oxidative stress. In conclusion, our results suggest that JNK and ERK1/2 signal pathways, which are activated via ROS, play a crucial role in neuronal apoptosis induced by oxidative stress.

How scaffolds shape MAPK signaling: what we know and opportunities for systems approaches

Scaffolding proteins add a new layer of complexity to the dynamics of cell signaling. Above their basic function to bring several components of a signaling pathway together, recent experimental research has found that scaffolds influence signaling in a much more complex way: scaffolds can exert some catalytic function, influence signaling by allosteric mechanisms, are feedback-regulated, localize signaling activity to distinct regions of the cell or increase pathway fidelity. Here we review experimental and theoretical approaches that address the function of two MAPK scaffolds, Ste5, a scaffold of the yeast mating pathway and KSR1/2, a scaffold of the classical mammalian MAPK signaling pathway. For the yeast scaffold Ste5, detailed mechanistic models have been valuable for the understanding of its function. For scaffolds in mammalian signaling, however, models have been rather generic and sketchy. For example, these models predicted narrow optimal scaffold concentrations, but when revisiting these models by assuming typical concentrations, rather a range of scaffold levels optimally supports signaling. Thus, more realistic models are needed to understand the role of scaffolds in mammalian signal transduction, which opens a big opportunity for systems biology.

Molecular cloning and characterization of a cDNA encoding extracellular signal-regulated kinase from Litopenaeus vannamei

Extracellular signal-regulated kinase (ERK) is a serine/threonine-specific kinase, which is activated by downstream signaling molecules of cellular activation, cytokine and chemokine stimulation and various other stimuli. Here we cloned an ERK gene from Litopenaeus vannamei and designated it as lverk. The lverk cDNA contained an open reading frame of 1098 bp encoding 365 amino acids. LVERK had a conserved TEY motif and serine/threonine protein kinase (S_TKc) domain, and close phylogenetic relationship to Penaeus monodon and Marsupenaeus japonicus ERK. Immunofluorescence staining analysis showed that following serum stimulation LVERK was located in cytoplasm and nucleus, but phospho-LVERK was prominently in nucleus, suggesting conserved ERK signaling module occurred in shrimp cells. Then during the white spot syndrome virus (WSSV) infection, LVERK and phospho-LVERK increased at the early stage of infection. Once silencing of lverk in vivo, the replication of WSSV was obviously inhibited. Moreover, treatment of mitogen-activated protein kinase kinase inhibitor in vitro could result in reduction of WSSV proliferation and delay of viral early gene transcription. Our results indicated a role of LVERK involved in WSSV infection. Understanding how WSSV influences ERK signaling pathway to dismantle an effective immune response may lead to insight into pathogenic progression and possible disease control.

Extracellular signal-regulated kinase 2 (ERK2) mediates phosphorylation and inactivation of nuclear interaction partner of anaplastic lymphoma kinase (NIPA) at G2/M

NIPA is an F-box-like protein that contributes to the timing of mitotic entry. It targets nuclear cyclin B1 for ubiquitination in interphase, whereas in G(2)/M phase, NIPA is inactivated by phosphorylation to allow for cyclin B1 accumulation, a critical event for proper G(2)/M transition. We recently specified three serine residues of NIPA and demonstrated a sequential phosphorylation at G(2)/M, where initial Ser-354 and Ser-359 phosphorylation is most crucial for SCF(NIPA) inactivation. In this study, we identified ERK2 as the kinase responsible for this critical initial phosphorylation step. Using in vitro kinase assays, we found that both ERK1 and ERK2 phosphorylated NIPA with high efficiency. Mutation of either Ser-354 or Ser-359 abolished ERK-dependent NIPA phosphorylation. Pharmacologic inhibition of ERK1/2 in cell lines resulted in decreased NIPA phosphorylation at G(2)/M. By combining cell cycle synchronization with stable expression of shRNA targeting either ERK1 or ERK2, we showed that ERK2 but not ERK1 mediated NIPA inactivation at G(2)/M. ERK2 knockdown led to a delay at the G(2)/M transition, a phenotype also observed in cells expressing a phospho-deficient mutant of NIPA. Thus, our data add to the recently described divergent functions of ERK1 and ERK2 in cell cycle regulation, which may be due in part to the differential ability of these kinases to phosphorylate and inactivate NIPA at G(2)/M.