Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data

Background

High-throughput genotype (HTG) data has been used primarily in genome-wide association (GWA) studies; however, GWA results explain only a limited part of the complete genetic variation of traits. In systems genetics, network approaches have been shown to be able to identify pathways and their underlying causal genes to unravel the biological and genetic background of complex diseases and traits, e.g., the Weighted Gene Co-expression Network Analysis (WGCNA) method based on microarray gene expression data. The main objective of this study was to develop a scale-free weighted genetic interaction network method using whole genome HTG data in order to detect biologically relevant pathways and potential genetic biomarkers for complex diseases and traits.

Results

We developed the Weighted Interaction SNP Hub (WISH) network method that uses HTG data to detect genome-wide interactions between single nucleotide polymorphism (SNPs) and its relationship with complex traits. Data dimensionality reduction was achieved by selecting SNPs based on its: 1) degree of genome-wide significance and 2) degree of genetic variation in a population. Network construction was based on pairwise Pearson's correlation between SNP genotypes or the epistatic interaction effect between SNP pairs. To identify modules the Topological Overlap Measure (TOM) was calculated, reflecting the degree of overlap in shared neighbours between SNP pairs. Modules, clusters of highly interconnected SNPs, were defined using a tree-cutting algorithm on the SNP dendrogram created from the dissimilarity TOM (1-TOM). Modules were selected for functional annotation based on their association with the trait of interest, defined by the Genome-wide Module Association Test (GMAT). We successfully tested the established WISH network method using simulated and real SNP interaction data and GWA study results for carcass weight in a pig resource population; this resulted in detecting modules and key functional and biological pathways related to carcass weight.

Conclusions

We developed the WISH network method which is a novel 'systems genetics' approach to study genetic networks underlying complex trait variation. The WISH network method reduces data dimensionality and statistical complexity in associating genotypes with phenotypes in GWA studies and enables researchers to identify biologically relevant pathways and potential genetic biomarkers for any complex trait of interest.

     

Safety,Pharmacokinetic, and Functional Effects of the Nogo-A Monoclonal Antibody in Amyotrophic Lateral Sclerosis: A Randomized,First-In-Human Clinical Trial

The neurite outgrowth inhibitor, Nogo-A, has been shown to be overexpressed in skeletal muscle in amyotrophic lateral sclerosis (ALS); it is both a potential biomarker and therapeutic target. We performed a double-blind, two-part, dose-escalation study, in subjects with ALS, assessing safety, pharmacokinetics (PK) and functional effects of ozanezumab, a humanized monoclonal antibody against Nogo-A. In Part 1, 40 subjects were randomized (3∶1) to receive single dose intravenous ozanezumab (0.01, 0.1, 1, 5, or 15 mg/kg) or placebo. In Part 2, 36 subjects were randomized (3∶1) to receive two repeat doses of intravenous ozanezumab (0.5, 2.5, or 15 mg/kg) or placebo, approximately 4 weeks apart. The primary endpoints were safety and tolerability (adverse events [AEs], vital signs, electrocardiogram (ECG), and clinical laboratory tests). Secondary endpoints included PK, immunogenicity, functional endpoints (clinical and electrophysiological), and biomarker parameters. Overall, ozanezumab treatment (0.01–15 mg/kg) was well tolerated. The overall incidence of AEs in the repeat dose 2.5 mg/kg and 15 mg/kg ozanezumab groups was higher than in the repeat dose placebo group and repeat dose 0.5 mg/kg ozanezumab group. The majority were considered not related to study drug by the investigators. Six serious AEs were reported in three subjects receiving ozanezumab; none were considered related to study drug. No study drug-related patterns were identified for ECG, laboratory, or vital signs parameters. One subject (repeat dose 15 mg/kg ozanezumab) showed a weak, positive anti-ozanezumab-antibody result. PK results were generally consistent with monoclonal antibody treatments. No apparent treatment effects were observed for functional endpoints or muscle biomarkers. Immunohistochemical staining showed dose-dependent co-localization of ozanezumab with Nogo-A in skeletal muscle. In conclusion, single and repeat dose ozanezumab treatment was well tolerated and demonstrated co-localization at the site of action. These findings support future studies with ozanezumab in ALS.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00875446","term_id":"NCT00875446"}}NCT00875446 GSK-ClinicalStudyRegister.com GSK ID 111330     

Complex mixtures of antibodies generated from a single production qualitatively and quantitatively evaluated by native Orbitrap mass spectrometry

Composite antibody mixtures designed to combat diseases present a new, rapidly emerging technology in the field of biopharmaceuticals. The combination of multiple antibodies can lead to increased effector response and limit the effect of escape variants that can propagate the disease. However, parallel development of analytical technologies is required to provide fast, thorough, accurate, and robust characterization of these mixtures. Here, we evaluate the utility of native mass spectrometry on an Orbitrap platform with high mass resolving power to characterize composite mixtures of up to 15 separate antibodies. With this technique, unambiguous identification of each antibody in the mixtures was achieved. Mass measurements of the intact antibodies varied 7 ppm on average, allowing highly reproducible identification and quantitation of each compound in these complex mixtures. We show that with the high mass-resolving power and robustness of this technology, high-resolution native mass spectrometry can be used efficiently even for batch-to-batch characterization.     

Research into the (Cost-) effectiveness of the ketogenic diet among children and adolescents with intractable epilepsy: design of a randomized controlled trial

Background  

Epilepsy is a neurological disorder, characterized by recurrent unprovoked seizures which have a high impact on the individual as well as on society as a whole. In addition to the economic burden, epilepsy imposes a substantial burden on the patients and their surroundings. Patients with uncontrolled epilepsy depend heavily on informal care and on health care professionals. About 30% of patients suffer from drug-resistant epilepsy. The ketogenic diet can be a treatment of last resort, especially for children. The beneficial effect of the ketogenic diet has been proven, but information is lacking about its cost-effectiveness. In the current study we will evaluate the (cost-) effectiveness of the ketogenic diet in children and adolescents with intractable epilepsy.     

Adults of European ant‐like stone beetles (Coleoptera: Staphylinidae: Scydmaeninae) Scydmaenus tarsatus Müller & Kunze and Scydmaenus hellwigii (Herbst) prey on soft‐bodied arthropods

Scydmaenine beetles are commonly described as predators specialized in capturing and feeding on armored mites of the order Oribatida, and documented cases of feeding on other live arthropods have not been known. Based on laboratory observations and a broad choice of Acari (armored and soft‐bodied) and other soil arthropods, food preferences and associated behavior of two scydmaenine species are clarified and described. Adults of Scydmaenus tarsatus ignored oribatid and mesostigmatan mites, but readily attacked and fed on a soft‐bodied Rhizoglyphus sp. (Acaridae), and on small springtails, especially on Ceratophysella denticulata (Hypogastruridae). A water drinking behavior was observed for this species, not reported previously in any Staphylinidae. Scydmaenus hellwigii ignored all tested Acari (including Rhizoglyphus) and scavenged on dead neanurine collembolans or freshly cut pieces of large springtails; a long term culture was maintained by feeding beetles with isotomid springtails. Previously reported strict specialization of Scydmaenus as a predator on Oribatida was not confirmed and it is concluded that the studied species feed on live soft‐bodied organisms and scavenge on dead arthropods.     

A specific inhibitor of the ubiquitin activating enzyme: synthesis and characterization of adenosyl-phospho-ubiquitinol, a nonhydrolyzable ubiquitin adenylate analogue

A nonhydrolyzable analogue of ubiquitin adenylate has been synthesized for use as a specific inhibitor of the ubiquitination of proteins. Ubiquitin adenylate is a tightly bound intermediate formed by the ubiquitin activating enzyme. The inhibitor adenosyl-phospho-ubiquitinol (APU) is the phosphodiester of adenosine and the C-terminal alcohol derived from ubiquitin. APU is isosteric with the normal reaction intermediate, the mixed anhydride of ubiquitin and AMP, but results from the replacement of the carbonyl oxygen of Gly76 with a methylene group. This stable analogue would be expected to bind to both ubiquitin and adenosine subsites and result in a tightly bound competitive inhibitor of ubiquitin activation. APU inhibits the ATP-PPi exchange reaction catalyzed by the purified ubiquitin activating enzyme in a manner competitive with ATP (Ki = 50 nM) and noncompetitive with ubiquitin (Ki = 35 nM). AMP has no effect on the inhibition, confirming that the inhibitor binds to the free form of the enzyme and not the thiol ester form. This inhibition constant is 10-fold lower than the dissociation constants for each substrate and 30-1000-fold lower than the respective Km values for ubiquitin and ATP. APU also effectively inhibits conjugation of ubiquitin to endogenous proteins catalyzed by reticulocyte fraction II with an apparent Ki of 0.75 microM. This weaker inhibition is consistent with the fact that activation of ubiquitin is not rate limiting in the conjugation reactions catalyzed by fraction II. APU is similarly effective as an inhibitor of the ubiquitin-dependent proteolysis of beta-lactoglobulin.(ABSTRACT TRUNCATED AT 250 WORDS)     

Beetles with ‘trochantelli’: phylogeny of Cephenniini (Coleoptera: Staphylinidae: Scydmaeninae) focussing on Neotropical genera

Neotropical genera of Cephenniini characterized by an additional leg ‘segment’ (‘trochantellus’) are revised, and the following new taxa are described: Shyri gen.n. , Shyri pichincha sp.n. (type species of Shyri) (Ecuador), Shyri perversus sp.n. (Ecuador), Shyri quitu sp.n. (Ecuador), Shyri microphthalmus sp.n. (Ecuador), Monstrophennium gen.n. (type species: Cephennium spinicolle Schaufuss), Furcodes gen.n. , Furcodes apicalis sp.n. (type species of Furcodes) (Mexico), Furcodes tutule sp.n. (Honduras), Paracephennium pumilio sp.n. (Costa Rica), Pseudocephennium iwokramanum sp.n. (Guyana), Pseudocephennium trilineatum sp.n. (Guyana), Pseudocephennium araguanum sp.n. (Venezuela), Pseudocephennium maximum sp.n. (Venezuela), Pseudocephennium peruvianum sp.n. (Peru), Pseudocephennium cochabambanum sp.n. (Bolivia), Pseudocephennium saramaccanum sp.n. (Suriname) and Pseudocephennium brokopondonum sp.n. (Suriname). Pseudocephennium spinicolle (Schaufuss) is transferred to Monstrophennium. Cladistic analysis of characters from adult morphology of all genera of Cephenniini and a large outgroup sample from Cyrtoscydmini, Eutheiini, Scydmaenini, Clidicini and Mastigini strongly supported the monophyly of Cephenniini. However, only the Cephennomicrus group comprising nine genera was strongly supported as a monophyletic clade, while only weak support was found for the previously suggested Cephennodes group and Cephennium group. Two alternative hypotheses concerning the phylogeny of Cephenniini are put forward and discussed: (i) the Cephennium group is sister to all remaining Cephenniini; or (ii) the Cephennomicrus group is sister to all remaining Cephenniini. The Neotropical genera with ‘trochantellus’ form a well‐supported clade derived from the ancestral lineage of the Cephennodes group.