IGFBP7 and GDF-15, but not P1NP, are associated with cardiac alterations and 10-year outcome in an elderly community-based study.

BACKGROUND: Little is known about the clinical value of Insulin-like growth factor-binding protein-7 (IGFBP7), a cellular senescence marker, in an elderly general population with multiple co-morbidities and high prevalence of asymptomatic cardiovascular ventricular dysfunction. Inflammation and fibrosis are hallmarks of cardiac aging and remodelling. Therefore, we assessed the clinical performance of IGFBP7 and two other biomarkers reflecting these pathogenic pathways, the growth differentiation factor-15 (GFD-15) and amino-terminal propeptide of type I procollagen (P1NP), for their association with cardiac phenotypes and outcomes in the PREDICTOR study. METHODS: 2001 community-dwelling subjects aged 65-84 years who had undergone centrally-read echocardiography, were selected through administrative registries. Atrial fibrillation (AF) and 4 echocardiographic patterns were assessed: E/e' (> 8), enlarged left atrial area, left ventricular hypertrophy (LVH) and reduced midwall circumference shortening (MFS). All-cause and cardiovascular mortality and hospitalization were recorded over a median follow-up of 10.6 years. RESULTS: IGFBP7 and GDF-15, but not P1NP, were independently associated with prevalent AF and echocardiographic variables after adjusting for age and sex. After adjustment for clinical risk factors and cardiac patterns or NT-proBNP and hsTnT, both IGFBP7 and GDF-15 independently predicted all-cause mortality, hazard ratios 2.13[1.08-4.22] and 2.03[1.62-2.56] per unit increase of Ln-transformed markers, respectively. CONCLUSIONS: In a community-based elderly cohort, IGFBP7 and GDF-15 appear associated to cardiac alterations as well as to 10-year risk of all-cause mortality.

The similarity of inherited diseases (I): clinical similarity within the phenotypic series.

BACKGROUND: Mutations of different genes often result in clinically similar diseases. Among the datasets of similar diseases, we analyzed the 'phenotypic series' from Online Mendelian Inheritance in Man and examined the similarity of the diseases that belong to the same phenotypic series, because we hypothesize that clinical similarity may unveil shared pathogenic mechanisms. METHODS: Specifically, for each pair of diseases, we quantified their similarity, based on both number and information content of the shared clinical phenotypes. Then, we assembled the disease similarity network, in which nodes represent diseases and edges represent clinical similarities. RESULTS: On average, diseases have high similarity with other diseases of their own phenotypic series, even though about one third of diseases have their maximal similarity with a disease of another series. Consequently, the network is assortative (i.e., diseases belonging to the same series link preferentially to each other), but the series differ in the way they distribute within the network. Specifically, heterophobic series, which minimize links to other series, form islands at the periphery of the network, whereas heterophilic series, which are highly inter-connected with other series, occupy the center of the network. CONCLUSIONS: The finding that the phenotypic series display not only internal similarity (assortativity) but also varying degrees of external similarity (ranging from heterophobicity to heterophilicity) calls for investigation of biological mechanisms that might be shared among different series. The correlation between the clinical and biological similarities of the phenotypic series is analyzed in Part II of this study1.

The similarity of inherited diseases (II): clinical and biological similarity between the phenotypic series.

BACKGROUND: Despite being caused by mutations in different genes, diseases in the same phenotypic series are clinically similar, as reported in Part I of this study. Here, in Part II, we hypothesized that the phenotypic series too might be clinically similar. Furthermore, on the assumption that gene mutations indirectly cause clinical phenotypes by directly affecting biological functions, we hypothesized that clinically similar phenotypic series might be biologically similar as well. METHODS: To test these hypotheses, we generated a clinical similarity network and a set of biological similarity networks. In both types of network, the nodes represent the phenotypic series, and the edges linking the nodes indicate the similarity of the linked phenotypic series. The weight of each edge is proportional to a similarity coefficient, which depends on the clinical phenotypes and the biological features that are shared by the linked phenotypic series, in the clinical and biological similarity networks, respectively. RESULTS: After assembling and analyzing the networks, we raised the threshold for the similarity coefficient, to retain edges of progressively greater weight. This way all the networks were gradually split into fragments, composed of phenotypic series with increasingly greater degrees of similarity. Finally, by comparing the fragments from the two types of network, we defined subsets of phenotypic series with varying types and degrees of clinical and biological correlation. CONCLUSIONS: Like the individual diseases, the phenotypic series too are clinically and biologically similar to each other. Furthermore, our findings unveil different modalities of correlation between the clinical manifestations and the biological features of the inherited diseases.

Quantitative analysis of proteins which are members of the same protein complex but cause locus heterogeneity in disease.

It is still largely unknown how mutations in different genes cause similar diseases - a condition known as locus heterogeneity. A likely explanation is that the different proteins encoded by the locus heterogeneity genes participate in the same biological function and, specifically, that they belong to the same protein complex. Here we report that, in up to 30% of the instances of locus heterogeneity, the disease-causing proteins are indeed members of the same protein complex. Moreover, we observed that, in many instances, the diseases and protein complexes only partially intersect. Among the possible explanations, we surmised that some genes that encode proteins in the complex have not yet been reported as causing disease and are therefore candidate disease genes. Mutations of known human disease genes and murine orthologs of candidate disease genes that encode proteins in the same protein complex do in fact often cause similar phenotypes in humans and mice. Furthermore, we found that the disease-complex intersection is not only incomplete but also non-univocal, with many examples of one disease intersecting more than one protein complex or one protein complex intersecting more than one disease. These limits notwithstanding, this study shows that action on proteins in the same complex is a widespread pathogenic mechanism underlying numerous instances of locus heterogeneity.

The drug prescription network: a system-level view of drug co-prescription in community-dwelling elderly people.

Networks are well suited to display and analyze complex systems that consist of numerous and interlinked elements. This study aimed at: (1) generating a series of drug prescription networks (DPNs) displaying co-prescription in community-dwelling elderly people; (2) analyzing DPN structure and organization; and (3) comparing various DPNs to unveil possible differences in drug co-prescription patterns across time and space. Data were extracted from the administrative prescription database of the Lombardy Region in northern Italy in 2000 and 2010. DPNs were generated, in which each node represents a drug chemical subclass, whereas each edge linking two nodes represents the co-prescription of the corresponding drugs to the same patient. At a global level, the DPN was a very dense and highly clustered network, whereas at the local level it was organized into anatomically homogeneous modules. In addition, the DPN was assortative by class, because similar nodes (representing drugs with the same anatomic, therapeutic, and pharmacologic annotation) connected to each other more frequently than expected, indicating that similar drugs are often co-prescribed. Finally, temporal changes in the co-prescription of specific drug sub-groups (for instance, proton pump inhibitors) translated into topological changes of the DPN and its modules. In conclusion, complementing more traditional pharmaco-epidemiology methods, the DPN-based method allows appreciatiation (and representation) of general trends in the co-prescription of a specific drug (e.g., its emergence as a heavily co-prescribed hub) in comparison with other drugs.

From networks of protein interactions to networks of functional dependencies.

BACKGROUND: As protein-protein interactions connect proteins that participate in either the same or different functions, networks of interacting and functionally annotated proteins can be converted into process graphs of inter-dependent function nodes (each node corresponding to interacting proteins with the same functional annotation). However, as proteins have multiple annotations, the process graph is non-redundant, if only proteins participating directly in a given function are included in the related function node. RESULTS: Reasoning that topological features (e.g., clusters of highly inter-connected proteins) might help approaching structured and non-redundant understanding of molecular function, an algorithm was developed that prioritizes inclusion of proteins into the function nodes that best overlap protein clusters. Specifically, the algorithm identifies function nodes (and their mutual relations), based on the topological analysis of a protein interaction network, which can be related to various biological domains, such as cellular components (e.g., peroxisome and cellular bud) or biological processes (e.g., cell budding) of the model organism S. cerevisiae. CONCLUSIONS: The method we have described allows converting a protein interaction network into a non-redundant process graph of inter-dependent function nodes. The examples we have described show that the resulting graph allows researchers to formulate testable hypotheses about dependencies among functions and the underlying mechanisms.

Amyotrophic lateral sclerosis multiprotein biomarkers in peripheral blood mononuclear cells.

BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a fatal progressive motor neuron disease, for which there are still no diagnostic/prognostic test and therapy. Specific molecular biomarkers are urgently needed to facilitate clinical studies and speed up the development of effective treatments. METHODOLOGY/PRINCIPAL FINDINGS: We used a two-dimensional difference in gel electrophoresis approach to identify in easily accessible clinical samples, peripheral blood mononuclear cells (PBMC), a panel of protein biomarkers that are closely associated with ALS. Validations and a longitudinal study were performed by immunoassays on a selected number of proteins. The same proteins were also measured in PBMC and spinal cord of a G93A SOD1 transgenic rat model. We identified combinations of protein biomarkers that can distinguish, with high discriminatory power, ALS patients from healthy controls (98%), and from patients with neurological disorders that may resemble ALS (91%), between two levels of disease severity (90%), and a number of translational biomarkers, that link responses between human and animal model. We demonstrated that TDP-43, cyclophilin A and ERp57 associate with disease progression in a longitudinal study. Moreover, the protein profile changes detected in peripheral blood mononuclear cells of ALS patients are suggestive of possible intracellular pathogenic mechanisms such as endoplasmic reticulum stress, nitrative stress, disturbances in redox regulation and RNA processing. CONCLUSIONS/SIGNIFICANCE: Our results indicate that PBMC multiprotein biomarkers could contribute to determine amyotrophic lateral sclerosis diagnosis, differential diagnosis, disease severity and progression, and may help to elucidate pathogenic mechanisms.

Glial cells drive preconditioning-induced blood-brain barrier protection.

BACKGROUND AND PURPOSE: The cerebrovascular contribution to ischemic preconditioning (IPC) has been scarcely explored. Using in vivo and in vitro approaches, we investigated the involvement of the blood-brain barrier and the role of its cellular components. METHODS: Seven-minute occlusion of the right middle cerebral artery, used as in vivo IPC stimulus 4 days before permanent occlusion of the right middle cerebral artery, significantly reduced brain infarct size (8.45±0.7 versus 13.61±0.08 mm3 measured 7 days after injury) and preserved blood-brain barrier function (Evans blue leakage, 0.54±0.1 versus 0.89±0.1 ng/mg). Assessment of neuronal, endothelial, and glial gene expression revealed that IPC specifically increased glial fibrillary acidic protein mRNA, thus showing selective astrocyte activation in IPC-protected mice. RESULTS: The blood-brain barrier was modeled by coculturing murine primary brain microvessel endothelial and astroglial cells. One-hour oxygen-glucose deprivation (OGD), delivered 24 hours before a 5-hour OGD, acted as an IPC stimulus, significantly attenuating the reduction in transendothelial electric resistance (199.17±11.7 versus 97.72±3.4 Ωcm2) and the increase in permeability coefficients for sodium fluorescein (0.98±0.11×10(-3) versus 1.8±0.36×10(-3) cm/min) and albumin (0.12±0.01×10(-3) versus 0.29±0.07×10(-3) cm/min) induced by severe OGD. IPC also prevented the 5-hour OGD-induced disorganization of the tight junction proteins ZO-1 and claudin-5. IPC on glial (but not endothelial) cells alone preserved transendothelial electric resistance, permeability coefficients, and ZO-1 localization after 5 hours of OGD. Astrocyte metabolic inhibition by fluorocitrate abolished IPC protection, confirming the critical role of astrocytes. IPC significantly increased glial fibrillary acidic protein, interleukin-6, vascular endothelial growth factor-a, and ciliary neurotrophic factor gene expression after OGD in glial cells, indicating that multiple pathways mediate the glial contribution to IPC. CONCLUSIONS: Our data show that the blood-brain barrier can be directly preconditioned and that astrocytes are major mediators of IPC protection.

Effect of microtubule-targeting drugs on cell-cell and cell-matrix junctions in tumor epithelial cells.

In this study, we investigated the effects of microtubule-targeting drugs, which either destabilize (the Vinca alkaloid vincristine) or stabilize (the taxane derivative docetaxel) microtubules, on the cell-cell and cell-matrix adhesive junctions of Caco-2 tumor epithelial cells, using fluorescence imaging and functional assays. We found that, in sub-confluent (but not confluent) cells, vincristine (but not docetaxel) affected cell-cell junction morphology. Furthermore, docetaxel (but not vincristine) attenuated the formation of the peri-junctional actomyosin ring and enhanced the internalization of junctional adhesion molecule-A. However, these effects of vincristine and docetaxel did not translate into appreciable functional changes during the opening and resealing of the cell-cell junctions. We also found that vincristine caused enlargement of focal adhesions (the major cell-matrix junctions) without affecting cell adhesion onto the matrix. Thus, we conclude that the microtubule-targeting drugs interfere to variable degrees with the morphology and/or function of the cell-cell and cell-matrix adhesive junctions. In addition, the results highlight the importance of considering the cellular context and dynamics (e.g. cell confluence and junction opening, respectively), when determining the final effects of microtubule manipulation on cell adhesiveness.

Pathobiology of junctional adhesion molecules.

Junctional adhesion molecules are transmembrane proteins that belong to the immunoglobulin superfamily. In addition to their localization in close proximity to the tight junctions in endothelial and epithelial cells, junctional adhesion molecules are also expressed in circulating cells that do not form junctions, such as leukocytes and platelets. As a consequence, these proteins are associated not only with the permeability-regulating barrier function of the tight junctions, but also with other biologic processes, such as inflammatory reactions, responses to vascular injury, and tumor angiogenesis. Furthermore, because of their transmembrane topology, junctional adhesion molecules are poised both for receiving inputs from the cell interior (their expression, localization, and function being regulated in response to inflammatory cytokines and growth factors) and for translating extracellular adhesive events into functional responses. This review focuses on the different roles of junctional adhesion molecules in normal and pathologic conditions, with emphasis on inflammatory reactions and vascular responses to injury.

Interactions of the prion peptide (PrP 106-126) with brain capillary endothelial cells: coordinated cell killing and remodeling of intercellular junctions.

We studied here the interactions of PrP 106-126, a peptide corresponding to the prion protein (PrP) amyloidogenic region, with a blood-brain barrier in vitro model consisting of confluent porcine brain endothelial cells (PBEC). PrP 106-126 interacted selectively with PBEC via their luminal side, and caused cumulative cell death, as shown by lactate dehydrogenase release, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction, Caspase 3 induction and direct cell counting. In addition, PrP 106-126, but not its corresponding scrambled peptide, produced a 50% reduction of the trans-endothelial electrical resistance, while the PBEC maintained confluency. This process was accompanied by a 23% increase of PBEC average size and the selective disappearance from the cell borders of the junction proteins occludin, claudin-5 and VE-cadherin (but not ZO-1), as evaluated by immunostaining. These results fit with a mechanism by which PrP 106-126 initiates a coordinated cell killing process ultimately causing the remaining cells to undergo a coordinated remodeling of the intercellular junctions and an expansion of their cell territory.

Eicosapentaenoic acid inhibits endothelial cell migration in vitro.

BACKGROUND: As n-3 Polyunsaturated Fatty Acids exert a beneficial action on the cardiovascular system, it is important to investigate their effects on endothelial cell responses that (like migration) contribute to repairing vascular lesions. METHODS: To this purpose, using functional and morphological in vitro assays, we have examined the effect of n-3 Polyunsaturated Fatty Acids on the migration of endothelial cells. RESULTS: We report here that incubation of endothelial cells with n-3 Polyunsaturated Fatty Acids impaired cell migration into a wound, triggered peripheral distribution of focal adhesions and caused partial disassembly of actin filaments. We also found that eicosapentaenoic acid and docosahexaenoic acid exerted similar effects on the focal adhesions, but that eicosapentaenoic acid was sufficient for inhibiting cell migration. CONCLUSIONS: Given the importance of endothelial cell migration in the repair of vascular injuries, these in vitro findings call for in vivo evaluation of vascular repair in response to different dietary ratios of eicosapentaenoic to docosahexaenoic acid.

Network analysis of cell adhesion: Adhesomes as context-defined subnetworks.

Complex systems consisting of diverse interlinked elements are often represented as networks and are described according to the principles of network analysis. Among the networks of biological interest, several protein-protein interactomes have been reported in recent years, mostly in conjunction with high-throughput assays and extensive efforts of literature mining. The resulting global networks display well-defined topological properties and provide a comprehensive view of all the biological contexts in which a given interactome is involved. Global networks, however, do not provide enough information about the specific contexts, such as biological processes and subcellular compartments in which the individual interactions occur. Thus, to glean additional insights, it is often advantageous to extract context-defined local subnetworks from the global networks. Our recently published network analysis of the cell-cell adhesome, i.e., the protein-protein interaction subnetwork that underlies both the biological process of cell-cell adhesion and the subcellular compartment of the apical junctions in human epithelial cells, is an example of such context-defined approaches.

The protein interaction network of the epithelial junctional complex: a system-level analysis.

To acquire system-level understanding of the intercellular junctional complex, protein-protein interactions occurring at the junctions of simple epithelial cells have been examined by network analysis. Although proper hubs (i.e., very rare proteins with exceedingly high connectivity) were absent from the junctional network, the most connected (albeit nonhub) proteins displayed a significant association with essential genes and contributed to the "small world" properties of the network (as shown by in vivo and in silico deletion, respectively). In addition, compared with a random network, the junctional network had greater tendency to form modules and subnets of densely interconnected proteins. Module analysis highlighted general organizing principles of the junctional complex. In particular, two major modules (corresponding to the tight junctions and to the adherens junctions/desmosomes) were linked preferentially to two other modules that acted as structural and signaling platforms.

Structural organization of the tight junctions.

Tight junctions are the most apical organelle of the apical junctional complex and are primarily involved in the regulation of paracellular permeability and membrane polarity. Extensive research in the past two decades has identified not only the individual molecules of the tight junctions but also their mutual interactions, which are the focus of the present review article. While a complete map of the interactions among the tight junction molecules is probably far from being complete, the available evidence already allows outlining the general molecular architecture of the tight junctions. Here, with the aim of gaining deeper mechanistic understanding of tight junction assembly, regulation and function, we have subdivided the known molecular interactions into four major clusters that are centered on cell surface, polarity, cytoskeletal and signaling molecules.

Junctional adhesion molecule-A regulates cell migration and resistance to shear stress.

Junctional adhesion molecule-A (JAM-A) is an adhesive protein expressed in endothelial cells, epithelial cells, platelets, and some leukocytes. JAM-A localizes to the tight junctions between contacting endothelial and epithelial cells, where it contributes to cell-cell adhesion and to the control of paracellular permeability. JAM-A also regulates cell motility, even though the quantitative biophysical features have not been characterized. In this study, we evaluated the role of JAM-A in the regulation of cell motility using JAM-A-expressing and JAM-A-deficient murine endothelial cells. We report that, in the absence of shear stress, JAM-A absence increases cell motility by increasing directional persistence but not cell speed. In addition, in the presence of shear stress, JAM-A absence increases protrusion extension in the direction of flow and increased downstream cellular displacement (while, conversely, decreasing upstream displacement). All these effects of JAM-A absence are mitigated by the microtubule-stabilizing compound taxol. A motility- and microtubule-related function, integrin-mediated adhesiveness, was only slightly reduced in JAM-A-deficient cells compared with JAM-A-expressing cells. However, overexpression of JAM-A in the JAM-A-deficient cells increased integrin adhesiveness to the same levels as those observed in taxol-treated JAM-A-deficient cells. Taken together, these data indicate that JAM-A regulates cell motility by cooperating with microtubule-stabilizing pathways.

Endothelial tight junctions: permeable barriers of the vessel wall.

The endothelial lining of the vessel wall is a permeable barrier, which is located at the interface between the vascular and the perivascular compartments. Although the endothelium acts as an efficient barrier that strictly separates the two compartments, it may also act as a permeable filter which allows selective exchange of solutes and water between the luminal and abluminal sides of the barrier. Similarly to epithelia, also in the endothelium permeability follows two distinct routes, which have been termed transcellular pathway (across the apical and basolateral membranes of individual cells) and paracellular pathway (through the intercellular junctions and the lateral spaces between contacting cells). After an initial description of the two pathways, the review focuses on the cellular and molecular basis of the paracellular pathway, with emphasis on the role of intercellular tight junctions and tight junction-associated claudins. Finally, the signaling events that regulate paracellular permeability are discussed.

Opposite effects of tumor necrosis factor and soluble fibronectin on junctional adhesion molecule-A in endothelial cells.

Junctional adhesion molecule-A (JAM-A) regulates key inflammatory responses, such as edema formation and leukocyte transmigration. Although it has been reported that the inflammatory cytokine tumor necrosis factor (TNF) causes the disassembly of JAM-A from the intercellular junctions, the mechanism has not been elucidated fully. Here, we report that TNF enhances the solubility of JAM-A in Triton X-100 and increases the amount of Triton-soluble JAM-A dimers at the cell surface but does not change the total levels of cellular JAM-A. Thus we hypothesized that TNF causes the redistribution of JAM-A from the junctions to the cell surface and that junction disassembly is sufficient to account for JAM-A redistribution. Intriguingly, however, even after complete disassembly of the junctions (with EDTA and trypsin), higher levels of JAM-A are detectable at the cell surface (by FACS analysis) in cells that had been previously incubated in the presence of TNF than in its absence. Thus we propose that TNF causes not only the disassembly of JAM-A from the junctions and its subsequent redistribution to the cell surface but also its dispersal in such a way that JAM-A becomes more easily accessible to the antibodies used for FACS analysis. Finally, we evaluated whether soluble fibronectin might attenuate the effects of TNF on JAM-A, as some inflammatory conditions are associated with the depletion of plasma fibronectin. We found that fibronectin reduces the effect of TNF on the disassembly of JAM-A, but not on its dispersal, thus further stressing that disassembly and dispersal can be functionally dissociated.