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1.  From networks of protein interactions to networks of functional dependencies 
BMC Systems Biology  2012;6:44.
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.
doi:10.1186/1752-0509-6-44
PMCID: PMC3434018  PMID: 22607727
Protein interaction networks; Biological functions; Markov representations; Peroxisomes; Cell budding; Polarized growth; Saccharomyces cerevisiae
2.  Amyotrophic Lateral Sclerosis Multiprotein Biomarkers in Peripheral Blood Mononuclear Cells 
PLoS ONE  2011;6(10):e25545.
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.
doi:10.1371/journal.pone.0025545
PMCID: PMC3187793  PMID: 21998667
3.  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.
doi:10.1186/2040-2384-2-12
PMCID: PMC2914648  PMID: 20618952
4.  The Protein Interaction Network of the Epithelial Junctional Complex: A System-Level Analysis 
Molecular Biology of the Cell  2008;19(12):5409-5421.
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.
doi:10.1091/mbc.E08-05-0477
PMCID: PMC2592657  PMID: 18923145
5.  Network analysis of cell adhesion 
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.
PMCID: PMC2649292  PMID: 19704858
systems biology; network analysis; protein-protein interactions; cell adhesion; cell-cell junctions; tight junctions; adherens junctions; desmosomes and focal adhesions
6.  Increased DC trafficking to lymph nodes and contact hypersensitivity in junctional adhesion molecule-A–deficient mice 
Journal of Clinical Investigation  2004;114(5):729-738.
Junctional adhesion molecule-A (JAM-A) is a transmembrane adhesive protein expressed at endothelial junctions and in leukocytes. In the present work, we found that DCs also express JAM-A. To evaluate the biological relevance of this observation, Jam-A–/– mice were generated and the functional behavior of DCs in vitro and in vivo was studied. In vitro, Jam-A–/– DCs showed a selective increase in random motility and in the capacity to transmigrate across lymphatic endothelial cells. In vivo, Jam-A–/– mice showed enhanced DC migration to lymph nodes, which was not observed in mice with endothelium-restricted deficiency of the protein. Furthermore, increased DC migration to lymph nodes was associated with enhanced contact hypersensitivity (CHS). Adoptive transfer experiments showed that JAM-A–deficient DCs elicited increased CHS in Jam-A+/+ mice, further supporting the concept of a DC-specific effect. Thus, we identified here a novel, non-redundant role of JAM-A in controlling DC motility, trafficking to lymph nodes, and activation of specific immunity.
doi:10.1172/JCI200421231
PMCID: PMC514585  PMID: 15343392
7.  Keratinocyte junctions and the epidermal barrier 
The Journal of Cell Biology  2002;156(6):947-949.
Although intercellular junctions are known to be the major regulators of permeability of simple epithelia, they had not been thought to be important in regulating the permeability of stratified mammalian epithelia. Furuse et al. (2002)(this issue) demonstrate that functional tight junctions may indeed be a necessary part of the permeability barrier of the skin.
doi:10.1083/jcb.200202116
PMCID: PMC2173466  PMID: 11901163
8.  Phosphorylation of a Conserved Integrin α3 QPSXXE Motif Regulates Signaling, Motility, and Cytoskeletal EngagementV⃞ 
Molecular Biology of the Cell  2001;12(2):351-365.
Integrin α3A cytoplasmic tail phosphorylation was mapped to amino acid S1042, as determined by mass spectrometry, and confirmed by mutagenesis. This residue occurs within a “QPSXXE” motif conserved in multiple α chains (α3A, α6A, α7A), from multiple species. Phosphorylation of α3A and α6A did not appear to be directly mediated by protein kinase C (PKC) α, β, γ, δ, ε, ζ, or μ, or by any of several other known serine kinases, although PKC has an indirect role in promoting phosphorylation. A S1042A mutation did not affect α3-Chinese hamster ovary (CHO) cell adhesion to laminin-5, but did alter 1) α3-dependent tyrosine phosphorylation of focal adhesion kinase and paxillin (in the presence or absence of phorbol 12-myristate 13 acetate stimulation), and p130CAS (in the absence of phorbol 12-myristate 13 acetate stimulation), 2) the shape of cells spread on laminin-5, and 3) α3-dependent random CHO cell migration on laminin-5. In addition, S1042A mutation altered the PKC-dependent, ligand-dependent subcellular distribution of α3 and F-actin in CHO cells. Together, the results demonstrate clearly that α3A phosphorylation is functionally relevant. In addition, the results strongly suggest that α3 phosphorylation may regulate α3 integrin interaction with the cytoskeleton.
PMCID: PMC30948  PMID: 11179420

Results 1-8 (8)