Identification of novel therapeutics for complex diseases from genome-wide association data

Background

Human genome sequencing has enabled the association of phenotypes with genetic loci, but our ability to effectively translate this data to the clinic has not kept pace. Over the past 60 years, pharmaceutical companies have successfully demonstrated the safety and efficacy of over 1,200 novel therapeutic drugs via costly clinical studies. While this process must continue, better use can be made of the existing valuable data. In silico tools such as candidate gene prediction systems allow rapid identification of disease genes by identifying the most probable candidate genes linked to genetic markers of the disease or phenotype under investigation. Integration of drug-target data with candidate gene prediction systems can identify novel phenotypes which may benefit from current therapeutics. Such a drug repositioning tool can save valuable time and money spent on preclinical studies and phase I clinical trials.

Methods

We previously used Gentrepid (http://www.gentrepid.org) as a platform to predict 1,497 candidate genes for the seven complex diseases considered in the Wellcome Trust Case-Control Consortium genome-wide association study; namely Type 2 Diabetes, Bipolar Disorder, Crohn's Disease, Hypertension, Type 1 Diabetes, Coronary Artery Disease and Rheumatoid Arthritis. Here, we adopted a simple approach to integrate drug data from three publicly available drug databases: the Therapeutic Target Database, the Pharmacogenomics Knowledgebase and DrugBank; with candidate gene predictions from Gentrepid at the systems level.

Results

Using the publicly available drug databases as sources of drug-target association data, we identified a total of 428 candidate genes as novel therapeutic targets for the seven phenotypes of interest, and 2,130 drugs feasible for repositioning against the predicted novel targets.

Conclusions

By integrating genetic, bioinformatic and drug data, we have demonstrated that currently available drugs may be repositioned as novel therapeutics for the seven diseases studied here, quickly taking advantage of prior work in pharmaceutics to translate ground-breaking results in genetics to clinical treatments.

     

Animal movements in fire‐prone landscapes

Movement is a trait of fundamental importance in ecosystems subject to frequent disturbances, such as fire‐prone ecosystems. Despite this, the role of movement in facilitating responses to fire has received little attention. Herein, we consider how animal movement interacts with fire history to shape species distributions. We consider how fire affects movement between habitat patches of differing fire histories that occur across a range of spatial and temporal scales, from daily foraging bouts to infrequent dispersal events, and annual migrations. We review animal movements in response to the immediate and abrupt impacts of fire, and the longer‐term successional changes that fires set in train. We discuss how the novel threats of altered fire regimes, landscape fragmentation, and invasive species result in suboptimal movements that drive populations downwards. We then outline the types of data needed to study animal movements in relation to fire and novel threats, to hasten the integration of movement ecology and fire ecology. We conclude by outlining a research agenda for the integration of movement ecology and fire ecology by identifying key research questions that emerge from our synthesis of animal movements in fire‐prone ecosystems.     

A hybridization model forRhipicephalus appendiculatus andR. zambeziensis (Acarina: Ixodidae) using glucose-6-phosphate-isomerase isoenzymes

In the Eastern Province of Zambia,Rhipicephalus appendiculatus (Neumann) andR. zambeziensis (Walker) are sympatric. Intermediate forms as well as typical specimens are found. No morphological criteria could detect cross-breeding between these species in the field.Hybrids betweenR. appendiculatus andR. zambeziensis were produced and glucose-phosphate-isomerase (EC 5.3.1.9.; GPI) isoenzymes resolved by agarose electrophoresis. Phenotyping hybrids in the F1 and F2 generations was explained by the autosomal transmission of two loci of GPI-genes. Identification of some hybrid phenotypes offers the possibility of showing presently undetected hybridization in the field. A genetic model is proposed to explain the patterns.     

Properties of the Cell Walls of Lactococcus lactis subsp. cremoris SK110 and SK112 and Their Relation to Bacteriophage Resistance

Resistance of Lactococcus lactis subsp. cremoris SK110 to bacteriophage sk11G, encoded on the plasmid pSK112, is due to poor phage adsorption. Its phage-sensitive variant SK112, cured of pSK112, adsorbs phages effectively. Incubation of SK112 with concanavalin A remarkably reduced phage adsorption to this strain. This treatment also caused agglutination of SK112 that was not found with SK110, indicating different concanavalin A adsorption characteristics of cell walls of both strains. The differences between the two strains were reduced by a mild alkali treatment of cells. This resulted in a positive agglutination with concanavalin A for both strains and in parallel adsorption of phage sk11G to both. Moreover, isolated cell walls of the two strains were investigated, and both bound phage sk11G. These observations suggest the presence of phage receptor material in SK112 as well as in SK110. SK110 contained a relatively high level of bound galactose when compared with the phage-sensitive SK112. After the mild alkali treatment, however, the galactose content of SK110 was diminished such that it became comparable with that of SK112. It is hypothesized that the alkali treatment liberates a galactose-containing component from the cell wall and causes phage sensitivity in L. lactis subsp. cremoris SK110.     

Spirometric changes during exacerbations of COPD: a post hoc analysis of the WISDOM trial

Background

Exacerbations of chronic obstructive pulmonary disease (COPD) are associated with loss of lung function and poor outcomes for patients. However, there are limited data on the time course of changes in forced expiratory volume in 1?s (FEV₁) preceding the first reported symptom and after the start of an exacerbation.

Methods

WISDOM was a multinational, randomized, double-blind, active-controlled, 52-week study in patients with severe-to-very severe COPD. Patients received triple therapy (long-acting muscarinic antagonist and long-acting β₂-agonist/inhaled corticosteroid [ICS]) for 6?weeks, and were randomized to continue triple therapy or stepwise withdrawal of the ICS (dual bronchodilator group). After suitable training, patients performed daily spirometry at home using a portable, battery-operated spirometer. In the present post hoc analysis, patients who continued to perform daily home spirometry and completed at least one measurement per week for a 56-day period before and after the start of a moderate or severe exacerbation were included. Missing values were imputed by linear interpolation (intermittent), backfilling (beginning) or carry forward (end). Exacerbation onset was the first day of a reported symptom of exacerbation.

Results

Eight hundred and eighty-eight patients in the WISDOM study had a moderate/severe exacerbation after the complete ICS withdrawal visit; 360 of them contributed at least one FEV₁ measure per week for the 8?weeks before and after the event and are included in this analysis.Mean daily FEV₁ began to decline from approximately 2?weeks before the onset of symptoms of an exacerbation, dropping from 0.907?L (mean Days ??56 to ??36 before the exacerbation) to 0.860?L on the first day of the exacerbation. After the exacerbation, mean FEV₁ improved but did not return to pre-exacerbation levels (mean Days 36–56 after the exacerbation, 0.875?L).The pattern of FEV₁ changes around exacerbations was similar in the triple therapy and dual bronchodilator groups, and a similar pattern was seen in moderate and severe exacerbations when analysed separately.

Conclusions

Mean lung function starts to decline prior to the first reported symptoms of an exacerbation, and does not recover to pre-exacerbation levels 8?weeks after the event.

Trial registration

WISDOM (ClinicalTrials.gov number, NCT00975195).

     

Rapid Activation of Bone Morphogenic Protein 9 by Receptor-mediated Displacement of Pro-domains

By non-covalent association after proteolytic cleavage, the pro-domains modulate the activities of the mature growth factor domains across the transforming growth factor-β family. In the case of bone morphogenic protein 9 (BMP9), however, the pro-domains do not inhibit the bioactivity of the growth factor, and the BMP9·pro-domain complexes have equivalent biological activities as the BMP9 mature ligand dimers. By using real-time surface plasmon resonance, we could demonstrate that either binding of pro-domain-complexed BMP9 to type I receptor activin receptor-like kinase 1 (ALK1), type II receptors, co-receptor endoglin, or to mature BMP9 domain targeting antibodies leads to immediate and complete displacement of the pro-domains from the complex. Vice versa, pro-domain binding by an anti-pro-domain antibody results in release of the mature BMP9 growth factor. Based on these findings, we adjusted ELISA assays to measure the protein levels of different BMP9 variants. Although mature BMP9 and inactive precursor BMP9 protein were directly detectable by ELISA, BMP9·pro-domain complex could only be measured indirectly as dissociated fragments due to displacement of mature growth factor and pro-domains after antibody binding. Our studies provide a model in which BMP9 can be readily activated upon getting into contact with its receptors. This increases the understanding of the underlying biology of BMP9 activation and also provides guidance for ELISA development for the detection of circulating BMP9 variants.     

Plant defense and herbivore counter-defense: benzoxazinoids and insect herbivores

Benzoxazinoids are a class of indole-derived plant chemical defenses comprising compounds with a 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one skeleton and their derivatives. These phytochemicals are widespread in grasses, including important cereal crops such as maize, wheat and rye, as well as a few dicot species, and display a wide range of antifeedant, insecticidal, antimicrobial, and allelopathic activities. Although their overall effects against insect herbivores are frequently reported, much less is known about how their modes of action specifically influence insect physiology. The present review summarizes the biological activities of benzoxazinoids on chewing, piercing-sucking, and root insect herbivores. We show how within-plant distribution modulates the exposure of different herbivore feeding guilds to these defenses, and how benzoxazinoids may act as toxins, feeding deterrents and digestibility-reducing compounds under different conditions. In addition, recent results on the metabolism of benzoxazinoids by insects and their consequences for plant-herbivore interactions are addressed, as well as directions for future research.     

Fine-scale spatial genetic structure in the frankincense tree <Emphasis Type="Italic">Boswellia papyrifera</Emphasis> (Del.) Hochst. and implications for conservation

The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species’ biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in dry tropical forests from Ethiopia, Eritrea and Sudan and is an important source of frankincense, a highly valued aromatic resin obtained from the bark of the tree. This study assessed the genetic diversity and fine-scale spatial genetic structure (FSGS) of two cohorts (adults and seedlings) from two populations (Guba-Arenja and Kurmuk) in Western Ethiopia and inferred intra-population gene dispersal in the species, using microsatellite markers. The expected heterozygosity (H _E) was 0.664–0.724. The spatial analyses based on kinship coefficient (F _ij) revealed a significant positive genetic correlation up to a distance of 130 m. Spatial genetic structure was relatively weak (Sp = 0.002–0.014) indicating that gene dispersal is extensive within the populations. Based on the FSGS patterns found, we estimate indirectly gene dispersal distances of 103 and 124 m for the two populations studied. The high heterozygosity, the low fixation index and the low Sp values found in this study are consistent with outcrossing as the (predominant) mating system in B. papyrifera. We suggest that seed collection for ex situ conservation and reforestation programmes of B. papyrifera should use trees separated by distances of at least 100 m but preferably 150 m to limit genetic relatedness among seeds from different trees.     

Aromatase inhibition by R 76713: experimental and clinical pharmacology

R 76713 is a new non-steroidal compound which inhibits aromatase in vitro and in vivo with a potency of at least 1000-fold that of aminoglutethimide. In male cynomolgus monkeys peripheral conversion of labeled androstenedione to estrone is decreased by 85%, 4-5 h after a single intravenous dose of 0.003 mg/kg of R 76713, without altering steroid metabolic clearance rates. In rats fed a sodium-depleted diet for 3 weeks, plasma levels of aldosterone and plasma renin activity remain unchanged 2 h after a single oral dose of up to 20 mg/kg of R 76713. This confirms previous data on the selectivity of R 76713 for aromatase inhibition as compared to inhibition of other enzymes involved in steroid biosynthesis. In male volunteers, a single oral dose of 5 or 10 mg of R 76713 lowers median plasma estradiol levels from 70 pM to the detection limit of the assay (30 pM) 4 and 8 h after intake, whereas no important changes are detected after placebo administration. In 15 premenopausal female volunteers receiving a single oral dose of 20 mg of R 76713, mean plasma estradiol levels decrease from 415 pM (before) to 179, 149 and 185 pM respectively 4, 8 and 24 h after intake whereas they remain above 380 pM after placebo (n = 7).     

Distribution of the sites of alkaline phosphatase(s) activity in vegetative cells of Bacillus subtilis

Sites of alkaline phosphatase activity have been located by an electron microscopic histochemical (Gomori) technique in vegetative cells of a repressible strain SB15 of Bacillus subtilis, derepressed and repressed by inorganic phosphate, and in a mutant SB1004 which forms alkaline phosphatase in a medium high in phosphate. The sites of enzyme activity were revealed as discrete, dense, and largely spherical bodies of varying sizes (20 to 150 nm). Cells of both repressible and repression-resistant strains acted on a wide variety of phosphate esters (p-nitrophenylphosphate, beta-glycerophosphate, adenosine-5'-phosphate, glucose-6-phosphate, glucose-l-phosphate, adenosine triphosphate, and sodium pyrophosphate) to produce inorganic phosphorus under conditions of alkaline phosphatase assay [0.05 m tris(hydroxymethyl)aminomethane buffer (pH 8.4) containing 2 mm MgCl(2)]. The purified alkaline phosphatase also acted on all these esters, although much less effectively on adenosine triphosphate and sodium pyrophosphate than did the cells. Comparison of the relative utilization of the various substrates by repressed and derepressed cells and purified enzyme suggested the presence of multiple enzymes in the cells. Thus, the cytochemical method of trapping the newly generated inorganic phosphorus determines the location of an alkaline phosphatase of broad substrate profile, and in addition locates the sites of other enzymes generating inorganic phosphorus under identical conditions of assay. It is intriguing that all of these enzymes usually exist in a few clusters attached to the peripheral plasma membrane. In addition to this predominant location, there were a few sites of enzyme activity in the cytoplasm unattached to any discernible structure, and also in the cell wall of the repression-resistant and of the derepressed, repressible strains.