Integrity of actin fibers and microtubules influences metastatic tumor cell adhesion

Tumor cell adhesion within host organ microvasculature, its stabilization and invasion into host organ parenchyma appear to be important steps during formation of distant metastasis. These interactions of circulating tumor cells with the host organs occur in the presence of fluid shear forces and soluble and cellular environmental conditions of the blood that can modulate their cellular responses and possibly their metastatic efficiency. Cytoskeletal components, such as actin filaments and microtubules, can regulate biophysical characteristics and cellular signaling of the circulating cells. Therefore, we investigated the role of these cytoskeletal structures for early steps during metastasis formation in vivo and in vitro. Using an intravital observation technique, tumor cell adhesion of colon carcinoma cells within the hepatic microcirculation of rats and their invasion into liver parenchyma was observed. Disruption of actin filaments increased cell adhesion, whereas tubulin disruption inhibited adhesive interactions in vivo. The impairment of the cytoskeleton modulated adhesion-mediated cell signaling via focal adhesion kinase (FAK) and paxillin under flow conditions in vitro. In the presence of fluid flow, focal adhesions were enlarged and hyperphosphorylated, whereas stress fibers were reduced compared to static cell adhesion. Disruption of microtubules, however, partially inhibited these effects. Combining the in vivo and in vitro results, our study suggested that changes in cell rigidity and avidity of cell adhesion molecules after disruption of cytoskeletal components appear to be more important for initial adhesive interactions in vivo than their interference with adhesion-mediated cellular signal transduction.     

Identification of the beta1-integrin binding site on alpha-actinin by cryoelectron microscopy

Cell-matrix adhesions in migrating cells are usually mediated by integrins, alpha-beta heterodimeric transmembrane proteins that link extracellular matrix molecules such as fibronectin to the cytoskeleton. We have synthesized the cytoplasmic domain of the beta1-integrin (residues H738-K778) with a histidine tag at its N-terminus. The binding of this peptide to a lipid monolayer containing a chelated-nickel group (dimyristoylphosphatidyl choline-suberimide-nitriloacetic acid:nickel salt) mimics the native environment at the cytoplasmic leaflet of the plasma membrane. A Nanogold particle was covalently linked to cysteines introduced at the C-terminus and after residue T757 on the integrin peptide, and co-crystallized with chicken smooth muscle alpha-actinin. The 2-D arrays of the beta1-integrin-alpha-actinin complex were examined by cryoelectron microscopy, with and without the gold label. Averaged projections were calculated for each specimen along with a difference map to determine the relative position of the gold-labeled beta1-integrin peptide. The difference maps indicate that the beta1-integrin cytoplasmic domain binds alpha-actinin between the first and second, 3-helix motifs in the central rod domain.     

Network analysis and proteomic identification of vimentin as a key regulator associated with invasion and metastasis in human hepatocellular carcinoma cells

Poor prognoses have long been associated with the high relapse and metastasis of human hepatocellular carcinoma (HCC). To achieve long-term survival, it is necessary to identify new HCC biomarkers and investigate their roles in cell mobility and invasiveness. Of note, overexpression of vimentin (Vim) was significantly correlated with tumor nuclear grade (p=0.01) and the invasive potential, indicating that Vim may be a promising candidate in regulating HCC metastasis. RNA interference-mediated silencing of Vim (siVim) suppressed the invasive and migratory propensity, and matrix metalloproteinase (MMP)-9 activity, and elicited morphological changes in poorly differentiated SK-Hep-1 cells. Moreover, we performed a comprehensive proteomic analysis to survey global protein changes mediated by siVim in SK-Hep-1 cells. Significant changes in cytoskeleton protein but not messenger RNA levels encoding these targeted proteins were observed. All of the data in the current study and a network analysis implied that abolition of Vim may disturb the expression and stability of various cytoskeletal proteins through promoting the ubiquitin system, resulting in impaired cell adhesion and motility. Collectively, an integrated approach represents a modality to explore novel relationships in a proteome complex and highlights the functional roles of Vim in HCC metastasis. This article is part of a Special Issue entitled: Translational Proteomics.     

Roles of microfilaments and microtubules in paxillin dynamics

We investigated the roles of microfilaments and microtubules in the localization and tyrosine phosphorylation of paxillin, a focal adhesion-associated signaling molecule, in bovine aortic endothelial cells (BAECs). Paxillin tyrosine phosphorylation is inhibited by cytochalasin D (CD), but slightly increased by colchicine and paclitaxol (taxol). CD also caused an overall disassembly of paxillin-containing focal adhesions (paxillin-FAs) and translocation of paxillin to the cytoplasm and perinuclear region with a diffuse distribution. Meanwhile, colchicine and taxol caused a disassembly of paxillin-FAs from cell periphery and lamellipodia, and their assembly in cell center. These results indicate that actin filaments are important in paxillin assembly in the FAs of the whole ECs and that microtubules are critical in paxillin assembly in cell periphery and lamellipodia; thus the microfilaments and microtubules play differential roles in the dynamics of paxillin assembly/disassembly. Our findings also suggest that tyrosine phosphorylation is an important element in paxillin dynamics at FAs.     

Backbone 1H, 13C, and 15N NMR assignments of the tail domain of vinculin

Vinculin is an essential protein involved in linking the actin cytoskeleton to sites of cell-cell and cell-matrix adhesion. Here we report the majority of the backbone ¹H_N, ¹⁵N, ¹³C_α, ¹³CO, and side chain ¹³C_β NMR resonance assignments of the actin binding tail domain of vinculin (Vt).     

1H, 15N, and 13C NMR chemical shift assignments for the Ig3 domain of palladin

As part of our NMR structure determination of the palladin Ig3 domain, we report nearly complete NMR chemical shift assignments for the ¹H, ¹³C, and ¹⁵N nuclei.     

PREL1 provides a link from Ras signalling to the actin cytoskeleton via Ena/VASP proteins

Ena/VASP family proteins are important modulators of cell migration and localize to focal adhesions, stress fibres and the very tips of lamellipodia and filopodia. Proline-rich proteins like vinculin and zyxin are well established interaction partners, which mediate Ena/VASP-recruitment via their EVH1-domains to focal adhesions and stress fibres. However, it is still unclear, which binding partners Ena/VASP proteins may have at lamellipodia tips and how their recruitment to these cellular protrusions is regulated. Here, we report the identification of a novel protein with high similarity to the C. elegans MIG-10 protein, which we termed PREL1 (Proline Rich EVH1 Ligand). PREL1 is a 74 kDa protein and shares homology with the Grb7-family of signalling adaptors. We show that PREL1 directly binds to Ena/VASP proteins and co-localizes with them at lamellipodia tips and at focal adhesions in response to Ras activation. Moreover, PREL1 directly binds to activated Ras in a phosphoinositide-dependent manner. Thus, our data pinpoint PREL1 as the first direct link between Ras signalling and cytoskeletal remodelling via Ena/VASP proteins during cell migration and spreading.     

A computational model of cell migration coupling the growth of focal adhesions with oscillatory cell protrusions

Cell migration is a highly integrated process where actin turnover, actomyosin contractility, and adhesion dynamics are all closely linked. In this paper, we propose a computational model investigating the coupling of these fundamental processes within the context of spontaneous (i.e. unstimulated) cell migration. In the unstimulated cell, membrane oscillations originating from the interaction between passive hydrostatic pressure and contractility are sufficient to lead to the formation of adhesion spots. Cell contractility then leads to the maturation of these adhesion spots into focal adhesions. Due to active actin polymerization, which reinforces protrusion at the leading edge, the traction force required for cell translocation can be generated. Computational simulations first show that the model hypotheses allow one to reproduce the main features of fibroblast cell migration and established results on the biphasic aspect of the cell speed as a function of adhesion strength. The model also demonstrates that certain temporal parameters, such as the adhesion proteins recycling time and adhesion lifetimes, influence cell motion patterns, particularly cell speed and persistence of the direction of migration. This study provides some elements, which allow a better understanding of spontaneous cell migration and enables a first glance at how an individual cell would potentially react once exposed to a stimulus.     

Affinity separation and enrichment methods in proteomic analysis

Protein separation or enrichment is one of the rate-limiting steps in proteomic studies. Specific capture and removal of highly-abundant proteins (HAP) with large sample-handling capacities are in great demand for enabling detection and analysis of low-abundant proteins (LAP). How to grasp and enrich these specific proteins or LAP in complex protein mixtures is also an outstanding challenge for biomarker discovery and validation. In response to these needs, various approaches for removal of HAP or capture of LAP in biological fluids, particularly in plasma or serum, have been developed. Among them, immunoaffinity subtraction methods based upon polyclonal IgY or IgG antibodies have shown to possess unique advantages for proteomic analysis of plasma, serum and other biological samples. In addition, other affinity methods that use recombinant proteins, lectins, peptides, or chemical ligands have also been developed and applied to LAP capture or enrichment. This review discusses in detail the need to put technologies and methods in affinity subtraction or enrichment into a context of proteomic and systems biology as "Separomics" and provides a prospective of affinity-mediated proteomics. Specific products, along with their features, advantages, and disadvantages will also be discussed.     

A comparative proteomic analysis during urodele lens regeneration

To examine underlying mechanisms of urodele lens regeneration we have employed a proteomic analysis of 650 proteins involved in several signaling pathways. We compared expression of these proteins between the regeneration-competent dorsal iris and the regeneration-incompetent ventral iris in the newt. After a series of screenings we selected several proteins to evaluate their expression quantitatively on immunoblots. We then used these selected proteins to compare their expression between the dorsal iris of the newt and the iris of the axolotl, another urodele, which does not regenerate the lens. In the newt we find that most proteins are expressed in both dorsal and ventral iris, even though there is differential regulation. Moreover, several of these proteins are expressed in the axolotl iris as well and for some of them their expression is consistent with the regeneration potential.     

Comparative proteomic analysis for the insoluble fractions of colorectal cancer patients

We used label-free quantitative proteomics with the insoluble fractions from colorectal cancer (CRC) patients to gain further insight into the utility of profiling altered protein expression as a potential biomarker for cancer. The insoluble fractions were prepared from paired tumor/normal biopsies from 13 patients diagnosed with CRC (stages I to IV). Fifty-six proteins identified in data pooled from the 13 cases were differentially expressed between the tumor and adjacent normal tissue. The connections between these proteins are involved in reciprocal networks related to tumorigenesis, cancer incidence based on genetic disorder, and skeletal and muscular disorders. To assess their potential utility as biomarkers, the relative expression levels of the proteins were validated using personal proteomics and a heat map to compare five individual CRC samples with five normal tissue samples. Further validation of a panel of proteins (KRT5, JUP, TUBB, and COL6A1) using western blotting confirmed the differential expression. These proteins gave specific network information for CRC, and yielded a panel of novel markers and potential targets for treatment. It is anticipated that the experimental approach described here will increase our understanding of the membrane environment in CRC, which may provide direction for making diagnoses and prognoses through molecular biomarker targeting.     

Nitric-oxide Synthase-2 Linkage to Focal Adhesion Kinase in Neutrophils Influences Enzyme Activity and β2 Integrin Function

This investigation was to elucidate the basis for augmentation of nitric-oxide synthesis in neutrophils exposed to hyperbaric oxygen. Hyperoxia increases synthesis of reactive species leading to S-nitrosylation of β-actin, which causes temporary inhibition of β₂ integrin adherence. Impaired β₂ integrin function and actin S-nitrosylation do not occur in neutrophils from mice lacking type-2 nitric-oxide synthase (iNOS) or when incubated with 1400W, an iNOS inhibitor. Similarly, effects of hyperoxia were abrogated in cells depleted of focal adhesion kinase (FAK) by treatment with small inhibitory RNA and those exposed to a specific FAK inhibitor concurrent with hyperoxia. Nitric oxide production doubles within 10 min exposure to hyperoxia but declines to approximately half-maximum production over an additional 10 min. Elevated nitric oxide production did not occur after FAK depletion or inhibition, or when filamentous actin formation was inhibited by cytochalasin D. Intracellular content of iNOS triples over the course of a 45-min exposure to hyperoxia and iNOS dimers increase in a commensurate fashion. Confocal microscopy and immunoprecipitation demonstrated that co-localization/linkage of FAK, iNOS, and filamentous actin increased within 15 min exposure to hyperoxia but then decreased below the control level. Using isolated enzymes in ex vivo preparations an association between iNOS and filamentous actin mediated by FAK could be demonstrated and complex formation was impeded when actin was S-nitrosylated. We conclude that iNOS activity is increased by an FAK-mediated association with actin filaments but peak nitric oxide production is transient due to actin S-nitrosylation during exposure to hyperoxia.     

The Arp2/3 inhibitory protein Arpin is dispensable for chemotaxis

Arpin is an Arp2/3 inhibitory protein, which decreases the protrusion lifetime and hence directional persistence in the migration of diverse cells. Arpin is activated by the small GTPase Rac, which controls cell protrusion, thus closing a negative feedback loop that renders the protrusion intrinsically unstable. Because of these properties, it was proposed that Arpin might play a role in directed migration, where directional persistence has to be fine‐tuned. We report here, however, that Arpin‐depleted tumour cells and Arpin knock‐out Dictyostelium amoeba display no obvious defect in chemotaxis. These results do not rule out a potential role of Arpin in other systems, but argue against a general role of Arpin in chemotaxis.     

Role of zinc metallothionein-3 (ZnMt3) in epidermal growth factor (EGF)-induced c-Abl protein activation and actin polymerization in cultured astrocytes

Recent evidence indicates that zinc plays a major role in neurochemistry. Of the many zinc-binding proteins, metallothionein-3 (Mt3) is regarded as one of the major regulators of cellular zinc in the brain. However, biological functions of Mt3 are not yet well characterized. Recently, we found that lysosomal dysfunction in metallothionein-3 (Mt3)-null astrocytes involves down-regulation of c-Abl. In this study, we investigated the role of Mt3 in c-Abl activation and actin polymerization in cultured astrocytes following treatment with epidermal growth factor (EGF). Compared with wild-type (WT) astrocytes, Mt3-null cells exhibited a substantial reduction in the activation of c-Abl upon treatment with EGF. Consistent with previous studies, activation of c-Abl by EGF induced dissociation of c-Abl from F-actin. Mt3 added to astrocytic cell lysates bound F-actin, augmented F-actin polymerization, and promoted the dissociation of c-Abl from F-actin, suggesting a possible role for Mt3 in this process. Conversely, Mt3-deficient astrocytes showed significantly reduced dissociation of c-Abl from F-actin following EGF treatment. Experiments using various peptide fragments of Mt3 showed that a fragment containing the N-terminal TCPCP motif (peptide 1) is sufficient for this effect. Removal of zinc from Mt3 or pep1 with tetrakis(2-pyridylmethyl)ethylenediamine abrogated the effect of Mt3 on the association of c-Abl and F-actin, indicating that zinc binding is necessary for this action. These results suggest that ZnMt3 in cultured astrocytes may be a normal component of c-Abl activation in EGF receptor signaling. Hence, modulation of Mt3 levels or distribution may prove to be a useful strategy for controlling cytoskeletal mobilization following EGF stimulation in brain cells.     

An immunoaffinity purification method for the proteomic analysis of ubiquitinated protein complexes

Protein ubiquitination plays an important role in the regulation of many cellular processes, including protein degradation, cell cycle regulation, apoptosis, and DNA repair. To study the ubiquitin proteome we have established an immunoaffinity purification method for the proteomic analysis of endogenously ubiquitinated protein complexes. A strong, specific enrichment of ubiquitinated factors was achieved using the FK2 antibody bound to protein G-beaded agarose, which recognizes monoubiquitinated and polyubiquitinated conjugates. Mass spectrometric analysis of two FK2 immunoprecipitations (IPs) resulted in the identification of 296 FK2-specific proteins in both experiments. The isolation of ubiquitinated and ubiquitination-related proteins was confirmed by pathway analyses (using Ingenuity Pathway Analysis and Gene Ontology-annotation enrichment). Additionally, comparing the proteins that specifically came down in the FK2 IP with databases of ubiquitinated proteins showed that a high percentage of proteins in our enriched fraction was indeed ubiquitinated. Finally, assessment of protein–protein interactions revealed that significantly more FK2-specific proteins were residing in protein complexes than in random protein sets. This method, which is capable of isolating both endogenously ubiquitinated proteins and their interacting proteins, can be widely used for unraveling ubiquitin-mediated protein regulation in various cell systems and tissues when comparing different cellular states.     

Comparative proteomic analysis of mouse embryonic stem cells and neonatal-derived cardiomyocytes

Pluripotent embryonic stem cells (ESCs) spontaneously differentiate via embryo-like aggregates into cardiomyocytes. A thorough understanding of the molecular conditions in ESCs is necessary before other potential applications of these cells such as cell therapy can be materialized. We applied two dimensional electrophoresis to analyze and compare the proteome profiling of spontaneous mouse ESC-derived cardiomyocytes (ESC-DCs), undifferentiated mouse ESCs, and neonatal-derived cardiomyocytes (N-DCs). Ninety-five percent of the proteins detected on the ESC-DCs and N-DCs could be precisely paired with one other, whereas only twenty percent of the ESC proteins could be reliably matched with those on the ESC-DCs and N-DCSs, suggesting a striking similarity between them. Having identified sixty proteins in the said three cell types, we sought to provide possible explanations for their differential expression patterns and discuss their relevance to cell biology. This study provides a new insight into the gene expression pattern of differentiated cardiomyocytes and is further evidence for a close relation between ESC-DCs and N-DCSs.     

Evaluation of four phosphopeptide enrichment strategies for mass spectrometry-based proteomic analysis

Information about phosphorylation status can be used to prioritize and characterize biological processes in the cell. Various analytical strategies have been proposed to address the complexity of phosphorylation status and comprehensively identify phosphopeptides. In this study, we evaluated four strategies for phosphopeptide enrichment, using titanium dioxide (TiO₂) and Phos-tag ligand particles from in-gel or in-solution digests prior to mass spectrometry-based analysis. Using TiO₂ and Phos-tag magnetic beads, it was possible to enrich phosphopeptides from in-gel digests of phosphorylated ovalbumin separated by Phos-tag SDS-PAGE or in-solution serum digests, while minimizing non-specific adsorption. The tip-column strategy with TiO₂ particles enabled enrichment of phosphopeptides from in-solution digests of whole-cell lysates with high efficiency and selectivity. However, the tip-column strategy with Phos-tag agarose beads yielded the greatest number of identified phosphopeptides. The strategies using both types of tip columns had a high degree of overlap, although there were differences in selectivity between the identified phosphopeptides. Together, our results indicate that multi-enrichment strategies using TiO₂ particles and Phos-tag agarose beads are useful for comprehensive phosphoproteomic analysis.     

Effects of the Actin‐Stabilizing Drug,Jasplakinolide, on Pigment Granule Motility in Isolated Retinal Pigment Epithelial (RPE) Cells of Green Sunfish,Lepomis cyanellus

The retinal pigment epithelium (RPE) of teleosts contains pigment granules that migrate in response to changes in light condition. Dissociated, cultured RPE cells in vitro can be triggered to aggregate or disperse pigment granules by the application of cAMP or dopamine, respectively. Previous research using the actin‐disrupting drug, cytochalasin D, suggested that pigment granule motility is actin dependent. To further examine the role of actin in pigment granule motility, we tested the effects of the actin‐stabilizing drug, jasplakinolide, on pigment granule motility. Pigment granules in previously dispersed RPE cells remained dispersed after jasplakinolide exposure (0.1–1 μM), but the drug halted movement of most pigment granules and stimulated rapid bi‐directional movements in a small subset of granules. Jasplakinolide also blocked net pigment granule aggregation and interfered with the maintenance of full aggregation. Although jasplakinolide did not block pigment granule dispersion, it did alter the motility of dispersing granules compared to control cells; rather than the normal saltatory, primarily centrifugal movements, granules of jasplakinolide‐treated cells demonstrated slow, creeping centrifugal movements and more rapid bi‐directional movements. Jasplakinolide also altered cell morphology; the length and thickness of apical projections increased, and enlarged, paddle‐like structures, which contained F‐actin appeared at the tips of projections. Actin antibody labeling of jasplakinolide‐treated cells revealed a more reticulated network of actin compared to antibody‐labeled control cells. These results indicate that jasplakinolide‐induced disruption of the actin network compromises normal pigment granule dispersion and aggregation in isolated RPE cells, thus providing further evidence that these movements are actin dependent.     

Optimal isolation of mitochondria for proteomic analyses

Considering the key role of mitochondria in cellular (dys)functions, we compared a standard isolation protocol, followed by lysis in urea/detergent buffer, with a commercially available isolation buffer that rapidly yields a mitochondrial protein fraction. The standard protocol yielded significantly better overall resolution and coverage of both the soluble and membrane mitochondrial proteomes; although the kit was faster, it resulted in recovery of only approximately 56% of the detectable proteome. The quality of “omic” analysis depends on sample handling; for large-scale protein studies, well-resolved proteomes are highly dependent on the purity of starting material and the rigor of the extraction protocol.