Novel therapeutics for coronary artery disease from genome-wide association study data

BACKGROUND: Coronary artery disease (CAD), one of the leading causes of death globally, is influenced by both environmental and genetic risk factors. Gene-centric genome-wide association studies (GWAS) involving cases and controls have been remarkably successful in identifying genetic loci contributing to CAD. Modern in silico platforms, such as candidate gene prediction tools, permit a systematic analysis of GWAS data to identify candidate genes for complex diseases like CAD. Subsequent integration of drug-target data from drug databases with the predicted candidate genes can potentially identify novel therapeutics suitable for repositioning towards treatment of CAD. METHODS: Previously, we were able to predict 264 candidate genes and 104 potential therapeutic targets for CAD using Gentrepid (http://www.gentrepid.org), a candidate gene prediction platform with two bioinformatic modules to reanalyze Wellcome Trust Case-Control Consortium GWAS data. In an expanded study, using five bioinformatic modules on the same data, Gentrepid predicted 647 candidate genes and successfully replicated 55% of the candidate genes identified by the more powerful CARDIoGRAMplusC4D consortium meta-analysis. Hence, Gentrepid was capable of enhancing lower quality genotype-phenotype data, using an independent knowledgebase of existing biological data. Here, we used our methodology to integrate drug data from three drug databases: the Therapeutic Target Database, PharmGKB and Drug Bank, with the 647 candidate gene predictions from Gentrepid. We utilized known CAD targets, the scientific literature, existing drug data and the CARDIoGRAMplusC4D meta-analysis study as benchmarks to validate Gentrepid predictions for CAD. RESULTS: Our analysis identified a total of 184 predicted candidate genes as novel therapeutic targets for CAD, and 981 novel therapeutics feasible for repositioning in clinical trials towards treatment of CAD. The benchmarks based on known CAD targets and the scientific literature showed that our results were significant (p < 0.05). CONCLUSIONS: We have demonstrated that available drugs may potentially be repositioned as novel therapeutics for the treatment of CAD. Drug repositioning can save valuable time and money spent on preclinical and phase I clinical studies

Compton scattering beyond the impulse approximation

We treat the non-relativistic Compton scattering process in which an incoming photon scatters from an N-electron many-body state to yield an outgoing photon and a recoil electron, without invoking the commonly used frameworks of either the impulse approximation (IA) or the independent particle model (IPM). An expression for the associated triple differential scattering cross section is obtained in terms of Dyson orbitals, which give the overlap amplitudes between the N-electron initial state and the (N-1) electron singly ionized quantum states of the target. We show how in the high energy transfer regime, one can recover from our general formalism the standard IA based formula for the cross section which involves the ground state electron momentum density (EMD) of the initial state. Our formalism will permit the analysis and interpretation of electronic transitions in correlated electron systems via inelastic x-ray scattering (IXS) spectroscopy beyond the constraints of the IA and the IPM.Comment: 7 pages, 1 figur

Cancer-associated fibroblasts are positively correlated with metastatic potential of human gastric cancers

<p>Abstract</p> <p>Background</p> <p>The prognosis of gastric cancer patients is difficult to predict because of defects in establishing the surgical-pathological features. Cancer-associated fibroblasts (CAFs) have been found to play prominent role in promoting tumor growth, invasion and metastasis. Thus raises the hypothesis that the extent of CAFs prevalence may help to establish the prognosis of gastric cancer patients.</p> <p>Methods</p> <p>Immunochemistry and realtime-PCR experiments were carried out to compare the expression of proteins which are specific markers of CAFs or secreted by CAFs in the tumor and normal tissue specimens. The extent of CAFs' prevalence was graded according to immunochemical staining, and correlation was further analyzed between CAFs' prevalence and other tumor characteristics which may influence the prognosis of gastric cancer patients.</p> <p>Results</p> <p>Nearly 80 percent of normal gastric tissues were negative or weak positive for CAFs staining, while more than 60 percent of gastric cancer tissues were moderate or strong positive for CAFs staining. Realtime-PCR results also showed significant elevated expression of FAP, SDF-1 and TGF-β1 in gastric cancer tissues compared to normal gastric tissues. Further analysis showed that CAFs' prevalence was correlated with tumor size, depth of the tumor, lymph node metastasis, liver metastasis or peritoneum metastasis.</p> <p>Conclusions</p> <p>Reactive cancer associated fibroblasts (CAFs) were frequently accumulated in gastric cancer tissues, and the prevalence of CAFs was correlated with tumor size, depth of the tumor and tumor metastasis, thus give some supports for establishing the prognosis of the gastric cancer patients.</p

Phenotypic Overlap between MMP-13 and the Plasminogen Activation System during Wound Healing in Mice

BACKGROUND: Proteolytic degradation of extracellular matrix is a crucial step in the healing of incisional skin wounds. Thus, healing of skin wounds is delayed by either plasminogen-deficiency or by treatment with the broad-spectrum metalloproteinase (MP) inhibitor Galardin alone, while the two perturbations combined completely prevent wound healing. Both urokinase-type plasminogen activator and several matrix metallo proteinases (MMPs), such as MMP-3, -9 and -13, are expressed in the leading-edge keratinocytes of skin wounds, which may account for this phenotypic overlap between these classes of proteases. METHODOLOGY: To further test that hypothesis we generated Mmp13;Plau and Mmp13;Plg double-deficient mice in a cross between Mmp13- and Plau-deficient mice as well as Mmp13- and Plg-deficient mice. These mice were examined for normal physiology in a large cohort study and in a well-characterized skin wound healing model, in which we made incisional 20 mm-long full-thickness skin wounds. PRINCIPAL FINDINGS: While mice that are deficient in Mmp13 have a mean healing time indistinguishable to wild-type mice, wound healing in both Plau- and Plg-deficient mice is significantly delayed. Histological analysis of healed wounds revealed a significant increase in keratin 10/14 immunoreactive layers of kerationcytes in the skin surface in Mmp13;Plau double-deficient mice. Furthermore, we observe, by immunohistological analysis, an aberrant angiogenic pattern during wound healing induced by Plau-deficiency, which has not previously been described. CONCLUSIONS: We demonstrate a phenotypic overlap, defined as an additional delay in wound healing in the double-deficient mice compared to the individual single-deficient mice, between MMP-13 and the plasminogen activation system in the process of wound healing, but not during gestation and in postnatal development. Thus, a dual targeting of uPA and MMP-13 might be a possible future strategy in designing therapies aimed at tissue repair or other pathological processes, such as cancer invasion, where proteolytic degradation is a hallmark

Autonomic system management in mobile grid environments

Mobile device integration in grid environments is a challenge for many researchers. Due to the transient nature of mobile devices, service management is a critical, but often overlooked area of research. We propose a distributed broker responsible for the autonomic management of grid services. The broker provides self discovery and negotiation, self configuration and self healing for SOA based mobile grids. In this paper the design and prototype implementation of the broker is presented and the importance of autonomic grid service management is shown.<br /