Non Linear Programming (NLP) Formulation for Quantitative Modeling of Protein Signal Transduction Pathways

Modeling of signal transduction pathways plays a major role in understanding cells'' function and predicting cellular response. Mathematical formalisms based on a logic formalism are relatively simple but can describe how signals propagate from one protein to the next and have led to the construction of models that simulate the cells response to environmental or other perturbations. Constrained fuzzy logic was recently introduced to train models to cell specific data to result in quantitative pathway models of the specific cellular behavior. There are two major issues in this pathway optimization: i) excessive CPU time requirements and ii) loosely constrained optimization problem due to lack of data with respect to large signaling pathways. Herein, we address both issues: the former by reformulating the pathway optimization as a regular nonlinear optimization problem; and the latter by enhanced algorithms to pre/post-process the signaling network to remove parts that cannot be identified given the experimental conditions. As a case study, we tackle the construction of cell type specific pathways in normal and transformed hepatocytes using medium and large-scale functional phosphoproteomic datasets. The proposed Non Linear Programming (NLP) formulation allows for fast optimization of signaling topologies by combining the versatile nature of logic modeling with state of the art optimization algorithms.     

Catalytic antibodies and their applications in biotechnology: state of the art

Catalytic antibodies are immunoglobulins endowed with enzymatic properties. Discovered in the second part of the 1980s, the enthusiasm they initially aroused was counterbalanced by the difficulty of their production and their low catalytic rates. Nevertheless, improvements in expression systems and engineering technologies, combined with various studies suggesting that catalytic antibodies play a role in the immune system, have opened the way to new applications for these proteins. Herein we review catalytic antibodies from a biotechnological point of view, focusing our study on the different production methods, expression systems and their potential clinical applications dedicated to these proteins.     

Evolution of hemodynamic forces in the pulmonary tree with progressively worsening pulmonary arterial hypertension in pediatric patients

Biomechanics and Modeling in Mechanobiology - Pulmonary arterial hypertension (PAH) is characterized by pulmonary vascular remodeling resulting in right ventricular (RV) dysfunction and ultimately...     

Cells in 3D matrices under interstitial flow: Effects of extracellular matrix alignment on cell shear stress and drag forces

Interstitial flow is an important regulator of various cell behaviors both in vitro and in vivo, yet the forces that fluid flow imposes on cells embedded in a 3D extracellular matrix (ECM), and the effects of matrix architecture on those forces, are not well understood. Here, we demonstrate how fiber alignment can affect the shear and pressure forces on the cell and ECM. Using computational fluid dynamics simulations, we show that while the solutions of the Brinkman equation accurately estimate the average fluid shear stress and the drag forces on a cell within a 3D fibrous medium, the distribution of shear stress on the cellular surface as well as the peak shear stresses remain intimately related to the pericellular fiber architecture and cannot be estimated using bulk-averaged properties. We demonstrate that perpendicular fiber alignment of the ECM yields lower shear stress and pressure forces on the cells and higher stresses on the ECM, leading to decreased permeability, while parallel fiber alignment leads to higher stresses on cells and increased permeability, as compared to a cubic lattice arrangement. The Spielman–Goren permeability relationships for fibrous media agreed well with CFD simulations of flow with explicitly considered fibers. These results suggest that the experimentally observed active remodeling of ECM fibers by fibroblasts under interstitial flow to a perpendicular alignment could serve to decrease the shear and drag forces on the cell.     

MicroRNA miR-155 Inhibits Bone Morphogenetic Protein (BMP) Signaling and BMP-Mediated Epstein-Barr Virus Reactivation

MicroRNA miR-155 is expressed at elevated levels in human cancers including cancers of the lung, breast, colon, and a subset of lymphoid malignancies. In B cells, miR-155 is induced by the oncogenic latency gene expression program of the human herpesvirus Epstein-Barr virus (EBV). Two other oncogenic herpesviruses, Kaposi''s sarcoma-associated herpesvirus and Marek''s disease virus, encode functional homologues of miR-155, suggesting a role for this microRNA in the biology and pathogenesis of these viruses. Bone morphogenetic protein (BMP) signaling is involved in an array of cellular processes, including differentiation, growth inhibition, and senescence, through context-dependent interactions with multiple signaling pathways. Alteration of this pathway contributes to a number of disease states including cancer. Here, we show that miR-155 targets the 3′ untranslated region of multiple components of the BMP signaling cascade, including SMAD1, SMAD5, HIVEP2, CEBPB, RUNX2, and MYO10. Targeting of these mediators results in the inhibition of BMP2-, BMP6-, and BMP7-induced ID3 expression as well as BMP-mediated EBV reactivation in the EBV-positive B-cell line, Mutu I. Further, miR-155 inhibits SMAD1 and SMAD5 expression in the lung epithelial cell line A549, it inhibits BMP-mediated induction of the cyclin-dependent kinase inhibitor p21, and it reverses BMP-mediated cell growth inhibition. These results suggest a role for miR-155 in controlling BMP-mediated cellular processes, in regulating BMP-induced EBV reactivation, and in the inhibition of antitumor effects of BMP signaling in normal and virus-infected cells.Despite the limited genetic content of microRNAs, their pervasive role in controlling normal and pathology-associated cellular processes has become firmly established in recent years. The importance of microRNA dysregulation in cancer is well appreciated, and a number of oncomirs and tumor suppressor microRNAs have been identified (15). As a member of the oncomir class of microRNAs, miR-155 is implicated in lymphomagenesis and a wide array of nonlymphoid tumors including breast, colon, and lung (7, 16, 24, 39, 42, 43). Despite strong evidence implicating miR-155 in cancer etiology, the mechanisms through which miR-155 supports the tumor phenotype are unclear, possibly due to limited knowledge of how predicted targets may be involved in the phenotypic properties of cancer. On the other hand, miR-155''s roles in normal immune cell development and the adaptive immune response are much better understood (33, 41). These studies have demonstrated a critical role for miR-155 in immune cell activation and maturation. This evidence and other work (8, 40) have identified critical miR-155 targets whose downregulation is required for these processes.The Epstein-Barr virus (EBV) is a human DNA tumor virus that contributes to lymphoid and epithelial cell malignancies. As a herpesvirus, a unique aspect of the EBV infection cycle is the ability to exist in either a lytic replicative state or in a latent state in which no virus is produced. Depending in part on cell background, EBV utilizes multiple forms of latency gene expression programs. True latency and type I latency are defined by the expression of no protein coding genes or by expression of the episomal replication factor EBNA1 only. Type II latency is defined by the expression of EBNA1 and the latent membrane proteins, LMP1 and/or LMP2, and is the predominant form observed in epithelial tissues. Type III latency refers to expression of the full repertoire of latency genes, which are highly tumorigenic and are capable of growth-transforming naïve resting B cells. While this form of latency is not well tolerated in immunocompetent individuals except during early stages of infection (prior to the development of adaptive immunity to these proteins), type III latency-associated lymphoid malignancies are common in immunocompromised individuals. Expression of type III latency genes in B cells mimics antigen-dependent B-cell activation, and accompanying this activation is a substantial induction of miR-155 expression (17, 20, 23, 29, 44). While it is reasonable to assume that induction of miR-155 by the type III latency program plays a role in EBV-mediated B-cell activation and oncogenesis, little is known regarding the role of miR-155 in the virus life cycle or its tumor-promoting activities.Originally identified as cytokines critically involved in the regulation of osteogenic differentiation, bone morphogenetic proteins (BMPs) are now appreciated as having critical functions in a vast number of developmental processes. Dysregulation of BMP signaling is also implicated in disease states including cancer (1). The canonical signaling pathway stimulated by BMP receptor engagement is the phosphorylation of the SMADs (mothers against decapentaplegic homologs), SMAD1, SMAD5, and SMAD9, which facilitates active transport of these mediators from the cytoplasm to the nucleus, where they bind and activate cellular promoters. While these signaling mediators are considered to have fairly redundant activities, the influence of BMP activation can have widely distinct outcomes on a particular cell depending on cellular context (3, 27). These distinctions arise from the innate low-affinity DNA binding properties of SMADs and the concordant requirement for any of a broad range of cofactors that facilitate high-affinity binding to specific sets of promoters. Using this signaling mechanism, the phenotypic outcome of BMP receptor engagement is controlled by the level of activation of other signaling pathways and SMAD binding cofactors. While activation of BMP signaling appears to contribute to some cancer types, it inhibits other cancer types by promoting growth arrest and differentiation and by inducing senescence (1). In immune cells, BMP signaling has been shown by multiple groups to inhibit lymphocyte activation, maturation, and growth (2, 6, 13, 18, 19, 37). Here, we show that miR-155 inhibits BMP signaling by targeting multiple factors in the BMP signal transduction cascade. This function may be important during immune cell activation by preventing BMP from impeding this process, it may be important for the survival of EBV type III latency associated tumors by preventing BMP-mediated viral reactivation and cell death, and it may be relevant to other cancer types by blocking growth arrest properties of BMPs.     

Aurothiomalate inhibits transformed growth by targeting the PB1 domain of protein kinase Ciota

We recently identified the gold compound aurothiomalate (ATM) as a potent inhibitor of the Phox and Bem1p (PB1)-PB1 domain interaction between protein kinase C (PKC) iota and the adaptor molecule Par6. ATM also blocks oncogenic PKCiota signaling and the transformed growth of human lung cancer cells. Here we demonstrate that ATM is a highly selective inhibitor of PB1-PB1 domain interactions between PKCiota and the two adaptors Par6 and p62. ATM has no appreciable inhibitory effect on other PB1-PB1 domain interactions, including p62-p62, p62-NBR1, and MEKK3-MEK5 interactions. ATM can form thio-gold adducts with cysteine residues on target proteins. Interestingly, PKCiota (and PKCzeta) contains a unique cysteine residue, Cys-69, within its PB1 domain that is not present in other PB1 domain containing proteins. Cys-69 resides within the OPR, PC, and AID motif of PKCiota at the binding interface between PKCiota and Par6 where it interacts with Arg-28 on Par6. Molecular modeling predicts formation of a cysteinyl-aurothiomalate adduct at Cys-69 that protrudes into the binding cleft normally occupied by Par6, providing a plausible structural explanation for ATM inhibition. Mutation of Cys-69 of PKCiota to isoleucine or valine, residues frequently found at this position in other PB1 domains, has little or no effect on the affinity of PKCiota for Par6 but confers resistance to ATM-mediated inhibition of Par6 binding. Expression of the PKCiota C69I mutant in human non-small cell lung cancer cells confers resistance to the inhibitory effects of ATM on transformed growth. We conclude that ATM inhibits cellular transformation by selectively targeting Cys-69 within the PB1 domain of PKCiota.     

Phylogeography of the Indo‐West Pacific maskrays (Dasyatidae,Neotrygon): a complex example of chondrichthyan radiation in the Cenozoic

Maskrays of the genus Neotrygon (Dasyatidae) have dispersed widely in the Indo‐West Pacific being represented largely by an assemblage of narrow‐ranging coastal endemics. Phylogenetic reconstruction methods reproduced nearly identical and statistically robust topologies supporting the monophyly of the genus Neotrygon within the family Dasyatidae, the genus Taeniura being consistently basal to Neotrygon, and Dasyatis being polyphyletic to the genera Taeniurops and Pteroplatytrygon. The Neotrygon kuhlii complex, once considered to be an assemblage of color variants of the same biological species, is the most derived and widely dispersed subgroup of the genus. Mitochondrial (COI, 16S) and nuclear (RAG1) phylogenies used in synergy with molecular dating identified paleoclimatic fluctuations responsible for periods of vicariance and dispersal promoting population fragmentation and speciation in Neotrygon. Signatures of population differentiation exist in N. ningalooensis and N. annotata, yet a large‐scale geological event, such as the collision between the Australian and Eurasian Plates, coupled with subsequent sea‐level falls, appears to have separated a once homogeneous population of the ancestral form of N. kuhlii into southern Indian Ocean and northern Pacific taxa some 4–16 million years ago. Repeated climatic oscillations, and the subsequent establishment of land and shallow sea connections within and between Australia and parts of the Indo‐Malay Archipelago, have both promoted speciation and established zones of secondary contact within the Indian and Pacific Ocean basins.     

Cooperativity between the Ras-ERK and Rho-Rho kinase pathways in urokinase-type plasminogen activator-stimulated cell migration.

Binding of the urokinase-type plasminogen activator (uPA) to its receptor activates diverse cell signaling pathways. How these signals are integrated so that cell physiology is altered remains unclear. In this study, we demonstrated that migration of MCF-7 breast cancer cells and HT-1080 fibrosarcoma cells on serum-coated surfaces is stimulated by agents that activate ERK, including uPA, epidermal growth factor, and constitutively active MEK1. The promigratory activity of these agents was entirely blocked not only by the MEK-specific antagonist PD098059, but also by antagonists of the Rho-Rho kinase pathway, including Y-27632 and dominant-negative RhoA (RhoA-N19). uPA did not significantly increase the level of GTP-bound RhoA, suggesting that the constitutive activity of the Rho-Rho kinase pathway may be sufficient to support ERK-stimulated cell migration. Paradoxically, Y-27632 and RhoA-N19 increased ERK phosphorylation in MCF-7 cells, providing further evidence that ERK activation alone does not promote cell migration when Rho kinase is antagonized. When MCF-7 cell migration was stimulated by ERK-independent processes such as expression of the beta(3) integrin subunit or changing the substratum to type I collagen, Y-27632 and RhoA-N19 failed to inhibit the response. This study supports a model in which the Ras-ERK and Rho-Rho kinase pathways cooperate to promote cell migration. Neutralizing either pathway is sufficient to block the response to agents that stimulate cell migration by activating ERK.