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.

     

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.     

Novel platforms for vascular carriers with controlled geometry

The first-generation platforms for vascular drug delivery adopted spherical morphologies. These carriers relied primarily on the size dependence of the enhanced permeability and retention effect to passively target vasculature, resulting in inefficient delivery due to significant variation in endothelial permeability. Enhanced delivery typically requires active targeting via receptor-mediated endocytosis by surface conjugation of targeting ligands. However, vascular carriers (VCs) still face numerous challenges en route to reaching their targets before delivery. The control of carrier shape offers opportunities to overcome in vivo barriers and enhance vascular drug delivery. Geometric features influence the ability of carrier particles to navigate physiological flow patterns, evade biological clearance mechanisms, sustain circulation, adhere to the vascular surface, and finally transport across or internalize into the endothelium. Although previous formulation strategies limited the fabrication of nonspherical carriers, numerous recent advances in both top-down and bottom-up fabrication techniques have enabled shape modulation as a key design element. As part of a series on vascular drug delivery, this review focuses on recent developments in novel vascular platforms with controlled geometry that enhance or modulate delivery functions. Starting with an overview of controlled geometry platforms, we review their shape-dependent functional characteristics for each stage of their vascular journey in vivo. We sequentially explore carrier geometries that evade reticuloendothelial system uptake, display enhanced circulation persistence and margination dynamics in flow, encourage adhesion to the vascular surface or extravasation through endothelium, and impact extravascular transport and cell internalization. The eventual biodistribution of VCs results from the culmination of their successive navigation of all these barriers and is profoundly influenced by their morphology. To enhance delivery efficacy, carrier designs synergistically combining controlled geometry with standard drug delivery strategies such as targeting moieties, surface decorations, and bulk material properties are discussed. Finally, we speculate on possibilities for innovation, harnessing shape as a design parameter for the next generation of vascular drug delivery platforms.     

A mechanoresponsive cadherin-keratin complex directs polarized protrusive behavior and collective cell migration

Collective cell migration requires maintenance of adhesive contacts between adjacent cells, coordination of polarized cell protrusions, and generation of propulsive traction forces. We demonstrate that mechanical force applied locally to C-cadherins on single Xenopus mesendoderm cells is sufficient to induce polarized cell protrusion and persistent migration typical of individual cells within a collectively migrating tissue. Local tension on cadherin adhesions induces reorganization of the keratin intermediate filament network toward these stressed sites. Plakoglobin, a member of the catenin family, is localized to cadherin adhesions under tension and is required for both mechanoresponsive cell behavior and assembly of the keratin cytoskeleton at the rear of these cells. Local tugging forces on cadherins occur in vivo through interactions with neighboring cells, and these forces result in coordinate changes in cell protrusive behavior. Thus, cadherin-dependent force-inducible regulation of cell polarity in single mesendoderm cells represents an emergent property of the intact tissue.     

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.     

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.     

Ion transport across the frog olfactory mucosa: the basal and odorant-stimulated states

The Ussing method was adapted to study the basal electrolyte transfer as well as the events that occur upon odorant stimulation in frog olfactory mucosa. The unstimulated short-circuit current was due mainly to a furosemide-sensitive ion transport system on the apical side of the olfactory mucosa. This current was not amiloride sensitive. The current-voltage relationship of the unstimulated state was linear. That of the odorant-evoked current was non-linear and amiloride-sensitive. Ouabain caused collapse of both the unstimulated and odorant-stimulated short-circuit current. In this case, voltage-clamping the tissue to non-zero values restored the odorant-evoked current with polarity depending on that of the clamping voltage. This suggested that the direction of the current is determined by that of the sodium electrochemical potential difference. Our results indicate that the unstimulated short-circuit current occurs through an apical sodium cotransport system, while the odorant-evoked current is due to odorant-activated, passive sodium channels that are amiloride sensitive.