A fast approach to global alignment of protein-protein interaction networks.

BACKGROUND: Global network alignment has been proposed as an effective tool for computing functional orthology. Commonly used global alignment techniques such as IsoRank rely on a two-step process: the first step is an iterative diffusion-based approach for assigning similarity scores to all possible node pairs (matchings); the second step applies a maximum-weight bipartite matching algorithm to this similarity score matrix to identify orthologous node pairs. While demonstrably successful in identifying orthologies beyond those based on sequences, this two-step process is computationally expensive. Recent work on computation of node-pair similarity matrices has demonstrated that the computational cost of the first step can be significantly reduced. The use of these accelerated methods renders the bipartite matching step as the dominant computational cost. This motivates a critical assessment of the tradeoffs of computational cost and solution quality (matching quality, topological matches, and biological significance) associated with the bipartite matching step. In this paper we utilize the state-of-the-art core diffusion-based step in IsoRank for similarity matrix computation, and couple it with two heuristic bipartite matching algorithms - a matrix-based greedy approach, and a tunable, adaptive, auction-based matching algorithm developed by us. We then compare our implementations against the performance and quality characteristics of the solution produced by the reference IsoRank binary, which also implements an optimal matching algorithm. RESULTS: Using heuristic matching algorithms in the IsoRank pipeline exhibits dramatic speedup improvements; typically ×30 times faster for the total alignment process in most cases of interest. More surprisingly, these improvements in compute times are typically accompanied by better or comparable topological and biological quality for the network alignments generated. These measures are quantified by the number of conserved edges in the alignment graph, the percentage of enriched components, and the total number of covered Gene Ontology (GO) terms. CONCLUSIONS: We have demonstrated significant reductions in global network alignment computation times by coupling heuristic bipartite matching methods with the similarity scoring step of the IsoRank procedure. Our heuristic matching techniques maintain comparable - if not better - quality in resulting alignments. A consequence of our work is that network-alignment based orthologies can be computed within minutes (as compared to hours) on typical protein interaction networks, enabling a more comprehensive tuning of alignment parameters for refined orthologies.

Universal programmable quantum circuit schemes to emulate an operator.

Unlike fixed designs, programmable circuit designs support an infinite number of operators. The functionality of a programmable circuit can be altered by simply changing the angle values of the rotation gates in the circuit. Here, we present a new quantum circuit design technique resulting in two general programmable circuit schemes. The circuit schemes can be used to simulate any given operator by setting the angle values in the circuit. This provides a fixed circuit design whose angles are determined from the elements of the given matrix-which can be non-unitary-in an efficient way. We also give both the classical and quantum complexity analysis for these circuits and show that the circuits require a few classical computations. For the electronic structure simulation on a quantum computer, one has to perform the following steps: prepare the initial wave function of the system; present the evolution operator U = e(-iHt) for a given atomic and molecular Hamiltonian H in terms of quantum gates array and apply the phase estimation algorithm to find the energy eigenvalues. Thus, in the circuit model of quantum computing for quantum chemistry, a crucial step is presenting the evolution operator for the atomic and molecular Hamiltonians in terms of quantum gate arrays. Since the presented circuit designs are independent from the matrix decomposition techniques and the global optimization processes used to find quantum circuits for a given operator, high accuracy simulations can be done for the unitary propagators of molecular Hamiltonians on quantum computers. As an example, we show how to build the circuit design for the hydrogen molecule.

Role of synthetic genetic interactions in understanding functional interactions among pathways.

Synthetic genetic interactions reveal buffering mechanisms in the cell against genetic perturbations. These interactions have been widely used by researchers to predict functional similarity of gene pairs. In this paper, we perform a comprehensive evaluation of various methods for predicting co-pathway membership of genes based on their neighborhood similarity in the genetic network. We clearly delineate the scope of these methods and use it to motivate a rigorous statistical framework for quantifying the contribution of each pathway to the functional similarity of gene pairs. We then use our model to infer interdependencies among KEGG pathways. The resulting KEGG crosstalk map yields significant insights into the high-level organization of the genetic network and is used to explain the effective scope of genetic interactions for predicting co-pathway membership of gene pairs. A direct byproduct of this effort is that we are able to identify subsets of genes in each pathway that act as 'ports' for interaction across pathways.

Role of TL1A and its receptor DR3 in two models of chronic murine ileitis.

TL1A is a TNF-like cytokine that binds to the death-domain receptor (DR)3 and provides costimulatory signals to activated lymphocytes. Through this interaction, TL1A induces secretion of IFN-gamma and may, therefore, participate in the development of T helper-1-type effector responses. In this study, we investigated whether interactions between TL1A and DR3 are involved in the pathogenesis of chronic murine ileitis. We demonstrate that alternative splicing of DR3 mRNA takes place during the activation of lymphocytes, which results in up-regulation of the complete/transmembrane (tm) form of DR3. Using two immunogenetically distinct animal models of Crohn's disease, we demonstrate that induction of intestinal inflammation is associated with significant up-regulation of TL1A and tm DR3 in the inflamed mucosa. In addition, within isolated lamina propria mononuclear cells from mice with inflammation, TL1A is primarily expressed on CD11c(high) dendritic cells. We also report that TL1A acts preferentially on memory CD4(+)/CD45RB(lo) murine lymphocytes by significantly inducing their proliferation, whereas it does not affect the proliferation of the naïve CD4(+)/CD45RB(hi) T helper cell subpopulation. Finally, we demonstrate that TL1A synergizes with both the cytokine-dependent IL-12/IL-18 pathway and with low-dose stimulation of the T cell receptor to significantly induce the secretion of IFN-gamma via an IL-18-independent pathway. Our results raise the possibility that interaction(s) between TL1A expressed on antigen-presenting cells and tm DR3 on lymphocytes may be of particular importance for the pathogenesis of chronic inflammatory conditions that depend on IFN-gamma secretion, including inflammatory bowel disease. Blockade of the TL1A/DR3 pathway may, therefore, offer therapeutic opportunities in Crohn's disease.

Activation of p38 MAPK is a key step in tumor necrosis factor-mediated inflammatory bone destruction.

OBJECTIVE: To investigate whether activation of p38 MAPK is a crucial signaling factor in inflammatory bone destruction mediated by tumor necrosis factor (TNF). Mice overexpressing TNF were treated with 2 different inhibitors of p38 MAPK, and the effect of this treatment on joint inflammation and structural damage was assessed. METHODS: Human TNF-transgenic mice received systemic treatment with 2 different p38 MAPK inhibitors (RO4399247 and AVE8677). Treatment was started at the time of symptom onset and lasted for 6 weeks. Mice were assessed for clinical signs of arthritis, bone erosion, and cartilage damage. In addition, the effect of these inhibitors on osteoclast generation in vitro and in vivo was assessed. RESULTS: Both p38 MAPK inhibitors significantly reduced clinical signs of TNF-mediated arthritis. This was attributable to reducing synovial inflammation by 50% without affecting the cellular composition of the infiltrate. Synovial expression of interleukin-1 and RANKL was reduced upon p38 MAPK blockade, and activation of the molecular target MAPK-activated protein kinase 2 (MAPKAP-2) was also inhibited. Proteoglycan loss of articular cartilage was reduced by 50%, although p38 MAPK inhibition did not change matrix molecule synthesis by cultivated chondrocytes. Importantly, bone loss was almost completely prevented by p38 MAPK inhibition. The numbers of synovial osteoclasts and precursors were dramatically reduced, and both p38 MAPK inhibitors also inhibited in vitro osteoclastogenesis at micromolar concentrations and blocked activation of MAPKAP-2 as well as differentiation markers in cultured osteoclast precursors. CONCLUSION: These results suggest the major importance of p38 MAPK for TNF-mediated inflammatory bone destruction in arthritis and suggest that inhibition of p38 MAPK might be an important tool for reducing structural damage in rheumatoid arthritis.

Zoledronic acid protects against local and systemic bone loss in tumor necrosis factor-mediated arthritis.

OBJECTIVE: Increased osteoclast activity is a key factor in bone loss in rheumatoid arthritis (RA). This suggests that osteoclast-targeted therapies could effectively prevent skeletal damage in patients with RA. Zoledronic acid (ZA) is one of the most potent agents for blocking osteoclast function. We therefore investigated whether ZA can inhibit the bone loss associated with chronic inflammatory conditions. METHODS: Human tumor necrosis factor (TNF)-transgenic (hTNFtg) mice, which develop severe destructive arthritis as well as osteoporosis, were treated with phosphate buffered saline, single or repeated doses of ZA, calcitonin, or anti-TNF, at the onset of arthritis. RESULTS: Synovial inflammation was not affected by ZA. In contrast, bone erosion was retarded by a single dose of ZA (-60%) and was almost completely blocked by repeated administration of ZA (-95%). Cartilage damage was partly inhibited, and synovial osteoclast counts were significantly reduced with ZA treatment. Systemic bone mass dramatically increased in hTNFtg mice after administration of ZA, which was attributable to an increase in trabecular number and connectivity. In addition, bone resorption parameters were significantly lowered after administration of ZA. Calcitonin had no effect on synovial inflammation, bone erosion, cartilage damage, or systemic bone mass. Anti-TNF entirely blocked synovial inflammation, bone erosion, synovial osteoclast formation, and cartilage damage but had only minor effects on systemic bone mass. CONCLUSION: ZA appears to be an effective tool for protecting bone from arthritic damage. In addition to their role in antiinflammatory drug therapy, modern bisphosphonates are promising candidates for maintaining joint integrity and reversing systemic bone loss in patients with arthritis.

Single and combined inhibition of tumor necrosis factor, interleukin-1, and RANKL pathways in tumor necrosis factor-induced arthritis: effects on synovial inflammation, bone erosion, and cartilage destruction.

OBJECTIVE: To investigate the efficacy of single and combined blockade of tumor necrosis factor (TNF), interleukin-1 (IL-1), and RANKL pathways on synovial inflammation, bone erosion, and cartilage destruction in a TNF-driven arthritis model. METHODS: Human TNF-transgenic (hTNFtg) mice were treated with anti-TNF (infliximab), IL-1 receptor antagonist (IL-1Ra; anakinra), or osteoprotegerin (OPG; an OPG-Fc fusion protein), either alone or in combinations of 2 agents or all 3 agents. Synovial inflammation, bone erosion, and cartilage damage were evaluated histologically. RESULTS: Synovial inflammation was inhibited by anti-TNF (-51%), but not by IL-1Ra or OPG monotherapy. The combination of anti-TNF with either IL-1Ra (-91%) or OPG (-81%) was additive and almost completely blocked inflammation. Bone erosion was effectively blocked by anti-TNF (-79%) and OPG (-60%), but not by IL-1Ra monotherapy. The combination of anti-TNF with IL-1Ra, however, completely blocked bone erosion (-98%). Inhibition of bone erosion was accompanied by a reduction of osteoclast numbers in synovial tissue. Cartilage destruction was inhibited by anti-TNF (-43%) and was weakly, but not significantly, inhibited by IL-1Ra, but was not inhibited by OPG monotherapy. The combination of anti-TNF with IL-1Ra was the most effective double combination therapy in preventing cartilage destruction (-80%). In all analyses, the triple combination of anti-TNF, IL-1Ra, and OPG was not superior to the double combination of anti-TNF and IL-1Ra. CONCLUSION: Articular changes caused by chronic overexpression of TNF are not completely blockable by monotherapies that target TNF, IL-1, or RANKL. However, combined approaches, especially the combined blockade of TNF and IL-1 and, to a lesser extent, TNF and RANKL, lead to almost complete remission of disease. Differences in abilities to block synovial inflammation, bone erosion, and cartilage destruction further strengthen the rationale for using combined blockade of more than one proinflammatory pathway.

Osteoprotegerin protects against generalized bone loss in tumor necrosis factor-transgenic mice.

OBJECTIVE: To investigate the role of tumor necrosis factor (TNF) in systemic bone loss of chronic inflammatory conditions, such as rheumatoid arthritis (RA), and to address the therapeutic potential of osteoclast blockade. METHODS: We investigated systemic bone changes in human TNF transgenic (hTNFtg) mice, which spontaneously developed severe inflammatory arthritis. RESULTS: Osteodensitometry revealed a significant decrease in trabecular bone mineral density (BMD) (-37%) in hTNFtg mice, and histomorphometry revealed a dramatic loss of bone volume (-85%) compared with wild-type controls. Osteoclast-covered bone surface and serum levels of deoxypyridinoline crosslinks were significantly elevated, suggesting increased osteoclast-mediated bone resorption in hTNFtg mice. Osteoprotegerin (OPG) completely blocked TNF-mediated bone loss by increasing BMD (+89%) and bone volume (+647%). Most strikingly, formation of primary spongiosa was dramatically increased (+563%) in hTNFtg mice after OPG treatment. Osteoclast-covered bone surface and serum levels of deoxypyridinoline crosslinks were significantly decreased by OPG, suggesting effective blockade of osteoclast-mediated bone resorption. OPG did not influence levels of hTNF, TNF receptor I (TNFRI), interleukin-1beta (IL-1beta), and IL-6. However, OPG decreased bone formation parameters (osteoblast-covered bone surface and serum osteocalcin levels), which were elevated in hTNFtg mice. In contrast to OPG, bisphosphonates and anti-TNF treatment did not affect generalized bone loss in hTNFtg mice. Anti-TNF, however, did not affect levels of TNF and TNFRI at the concentrations tested. These data indicate that generalized bone loss due to increased TNF can be blocked by OPG. CONCLUSION: OPG may represent a potent tool for preventing generalized loss of bone mass in chronic inflammatory disorders, especially RA.