Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes

It has been hypothesized that, in aggregate, rare variants in coding regions of genes explain a substantial fraction of the heritability of common diseases. We sequenced the exomes of 1,000 Danish cases with common forms of type 2 diabetes (including body mass index > 27.5 kg/m² and hypertension) and 1,000 healthy controls to an average depth of 56×. Our simulations suggest that our study had the statistical power to detect at least one causal gene (a gene containing causal mutations) if the heritability of these common diseases was explained by rare variants in the coding regions of a limited number of genes. We applied a series of gene-based tests to detect such susceptibility genes. However, no gene showed a significant association with disease risk after we corrected for the number of genes analyzed. Thus, we could reject a model for the genetic architecture of type 2 diabetes where rare nonsynonymous variants clustered in a modest number of genes (fewer than 20) are responsible for the majority of disease risk.     

Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery

Background

Different cell types have distinctive patterns of chromosome positioning in the nucleus. Although ectopic affinity-tethering of specific loci can be used to relocate chromosomes to the nuclear periphery, endogenous nuclear envelope proteins that control such a mechanism in mammalian cells have yet to be widely identified.

Results

To search for such proteins, 23 nuclear envelope transmembrane proteins were screened for their ability to promote peripheral localization of human chromosomes in HT1080 fibroblasts. Five of these proteins had strong effects on chromosome 5, but individual proteins affected different subsets of chromosomes. The repositioning effects were reversible and the proteins with effects all exhibited highly tissue-restricted patterns of expression. Depletion of two nuclear envelope transmembrane proteins that were preferentially expressed in liver each reduced the normal peripheral positioning of chromosome 5 in liver cells.

Conclusions

The discovery of nuclear envelope transmembrane proteins that can modulate chromosome position and have restricted patterns of expression may enable dissection of the functional relevance of tissue-specific patterns of radial chromosome positioning.     

The Nordic Aortic Valve Intervention (NOTION) trial comparing transcatheter versus surgical valve implantation: study protocol for a randomised controlled trial

Background

Degenerative aortic valve (AV) stenosis is the most prevalent heart valve disease in the western world. Surgical aortic valve replacement (SAVR) has until recently been the standard of treatment for patients with severe AV stenosis. Whether transcatheter aortic valve implantation (TAVI) can be offered with improved safety and similar effectiveness in a population including low-risk patients has yet to be examined in a randomised setting.

Methods/Design

This randomised clinical trial will evaluate the benefits and risks of TAVI using the transarterial CoreValve System (Medtronic Inc., Minneapolis, MN, USA) (intervention group) compared with SAVR (control group) in patients with severe degenerative AV stenosis. Randomisation ratio is 1:1, enrolling a total of 280 patients aged 70 years or older without significant coronary artery disease and with a low, moderate, or high surgical risk profile. Trial outcomes include a primary composite outcome of myocardial infarction, stroke, or all-cause mortality within the first year after intervention (expected rates 5% for TAVI, 15% for SAVR). Exploratory safety outcomes include procedure complications, valve re-intervention, and cardiovascular death, as well as cardiac, cerebral, pulmonary, renal, and vascular complications. Exploratory efficacy outcomes include New York Heart Association functional status, quality of life, and valve prosthesis and cardiac performance. Enrolment began in December 2009, and 269 patients have been enrolled up to December 2012.

Discussion

The trial is designed to evaluate the performance of TAVI in comparison with SAVR. The trial results may influence the choice of treatment modality for patients with severe degenerative AV stenosis.

Trial registration

ClinicalTrials.gov: NCT01057173     

Nanotopographical stimulation of mechanotransduction and changes in interphase centromere positioning

We apply a recently developed method for controlling the spreading of cultured cells using electron beam lithography (EBL) to create polymethylmethacrylate (PMMA) substrata with repeating nanostructures. There are indications that the reduced cell spreading on these substrata, compared with planar PMMA, results from a reduced adhesivity since there are fewer adhesive structures and fewer of their associated stress fibres. The reduced cell spreading also results in a reduced nuclear area and a closer spacing of centrosomes within the nucleus, suggesting that the tension applied to the nucleus is reduced as would be expected from the reduction in stress fibres. In order to obtain further evidence for this, we have used specific inhibitors of components of the cytoskeleton and have found effects comparable with those induced by the new substrata. We have also obtained evidence that these subtrata result in downregulation of gene expression which suggests that this may be due to the changed tension on the nucleus: an intriguing possibility that merits further investigation.     

Cofactory: Sequence‐based prediction of cofactor specificity of Rossmann folds

Obtaining optimal cofactor balance to drive production is a challenge in metabolically engineered microbial production strains. To facilitate identification of heterologous enzymes with desirable altered cofactor requirements from native content, we have developed Cofactory, a method for prediction of enzyme cofactor specificity using only primary amino acid sequence information. The algorithm identifies potential cofactor binding Rossmann folds and predicts the specificity for the cofactors FAD(H₂), NAD(H), and NADP(H). The Rossmann fold sequence search is carried out using hidden Markov models whereas artificial neural networks are used for specificity prediction. Training was carried out using experimental data from protein–cofactor structure complexes. The overall performance was benchmarked against an independent evaluation set obtaining Matthews correlation coefficients of 0.94, 0.79, and 0.65 for FAD(H₂), NAD(H), and NADP(H), respectively. The Cofactory method is made publicly available at http://www.cbs.dtu.dk/services/Cofactory . Proteins 2014; 82:1819–1828. © 2014 Wiley Periodicals, Inc.     

The Leukocyte Nuclear Envelope Proteome Varies with Cell Activation and Contains Novel Transmembrane Proteins That Affect Genome Architecture

A favored hypothesis to explain the pathology underlying nuclear envelopathies is that mutations in nuclear envelope proteins alter genome/chromatin organization and thus gene expression. To identify nuclear envelope proteins that play roles in genome organization, we analyzed nuclear envelopes from resting and phytohemagglutinin-activated leukocytes because leukocytes have a particularly high density of peripheral chromatin that undergoes significant reorganization upon such activation. Thus, nuclear envelopes were isolated from leukocytes in the two states and analyzed by multidimensional protein identification technology using an approach that used expected contaminating membranes as subtractive fractions. A total of 3351 proteins were identified between both nuclear envelope data sets among which were 87 putative nuclear envelope transmembrane proteins (NETs) that were not identified in a previous proteomics analysis of liver nuclear envelopes. Nuclear envelope localization was confirmed for 11 new NETs using tagged fusion proteins and antibodies on spleen cryosections. 27% of the new proteins identified were unique to one or the other of the two leukocyte states. Differences in expression between activated and resting leukocytes were confirmed for some NETs by RT-PCR, and most of these proteins appear to only be expressed in certain types of blood cells. Several known proteins identified in both data sets have functions in chromatin organization and gene regulation. To test whether the novel NETs identified might include those that also regulate chromatin, nine were run through two screens for different chromatin effects. One screen found two NETs that can recruit a specific gene locus to the nuclear periphery, and the second found a different NET that promotes chromatin condensation. The variation in the protein milieu with pharmacological activation of the same cell population and consequences for gene regulation suggest that the nuclear envelope is a complex regulatory system with significant influences on genome organization.The nuclear envelope (NE)1 is a double membrane system consisting of the intermediate filament nuclear lamin polymer and associated proteins attached to the inner nuclear membrane (INM) (1), nuclear pore complexes (NPCs) that direct transport of soluble macromolecules in and out of the nucleus (2), and the outer nuclear membrane (ONM) and associated proteins. Structurally, the ONM is continuous with the endoplasmic reticulum (ER) and is studded with ribosomes (3), yet it also contains unique proteins, many of which connect the cytoskeleton to the NE (4). On the other side, lamins and many INM proteins directly connect chromatin to the NE. Lamins and an increasing number of nuclear envelope transmembrane proteins (NETs) have been linked to a similarly increasing number of diseases ranging from muscular dystrophy to neuropathy, dermopathy, lipodystrophy, bone disorders, and progeroid aging syndromes (5, 6).A favored hypothesis to explain how different NE proteins can produce such a wide range of disease pathologies is that chromatin-NE connections are disrupted with NE protein mutations, yielding changes in gene regulation. This hypothesis is supported by observations that the distribution of dense peripheral chromatin is affected in fibroblasts from patients with NE-linked muscular dystrophy, cardiomyopathy, mandibuloacral dysplasia, and progeria (7–10). Furthermore, many binding partners have been identified for NETs that are either chromatin proteins, enzymes that modify chromatin proteins, or regulators of gene expression (1, 11). These include markers of silent chromatin such as heterochromatin protein 1 (12) and proteins that modify chromatin to a silent conformation such as histone deacetylase 3 (13). The importance of the NE to global genome organization has been underscored by several recent studies that showed that affinity-based recruitment of a specific chromosome locus by the NE both pulled entire chromosomes to the periphery and affected gene regulation in complex ways (14–16).To identify NE proteins likely to be involved in genome organization, we turned to lymphocytes as a model system. Lymphocytes in the resting state tend to have massive amounts of dense peripheral chromatin as determined by electron microscopy studies. Upon activation with phytohemagglutinin, this dense chromatin largely dissipates as the cells actively express genes (17–20). Thus, to identify proteins that might be involved in tethering heterochromatin to the NE or in changing its organization, we analyzed the NE proteomes of leukocyte populations (∼70% lymphocytes) in both the resting and phytohemagglutinin (PHA)-activated states. The previously validated subtractive approach was applied (21) using microsomes and mitochondria, the principal membrane contaminants expected, as subtractive fractions.Many new NE proteins were identified that had not been identified in previous NE proteomics investigations using liver and neuroblastoma cells (21, 22). NE residence was confirmed for 12 novel NETs by expression of epitope-tagged versions and using antibodies on tissue cryosections.Roughly one-quarter of the proteins identified varied between the resting and activated states. Some NET differences between the two data sets were confirmed by RT-PCR. Among the known proteins identified were several that suggest that changes in NE composition associated with PHA activation contribute to gene regulation. Novel NETs identified also appear to play significant roles in genome organization/regulation as we found that several can either recruit a specific locus to the nuclear periphery or promote chromatin condensation. As several studies have implicated misregulation of chromatin organization in NE diseases (7, 8), these newly identified NETs may contribute to the diverse pathologies associated with NE diseases.     

A bioluminescence resonance energy transfer 2 (BRET2) assay for monitoring seven transmembrane receptor and insulin receptor crosstalk

The angiotensin AT₁ receptor is a seven transmembrane (7TM) receptor, which mediates the regulation of blood pressure. Activation of angiotensin AT₁ receptor may lead to impaired insulin signaling indicating crosstalk between angiotensin AT₁ receptor and insulin receptor signaling pathways. To elucidate the molecular mechanisms behind this crosstalk, we applied the BRET² technique to monitor the effect of angiotensin II on the interaction between Rluc⁸ tagged insulin receptor and GFP² tagged insulin receptor substrates 1, 4, 5 (IRS1, IRS4, IRS5) and Src homology 2 domain-containing protein (Shc). We demonstrate that angiotensin II reduces the interaction between insulin receptor and IRS1 and IRS4, respectively, while the interaction with Shc is unaffected, and this effect is dependent on Gαq activation. Activation of other Gαq-coupled 7TM receptors led to a similar reduction in insulin receptor and IRS4 interactions whereas Gαs- and Gαi-coupled 7TM receptors had no effect. Furthermore, we used a panel of kinase inhibitors to show that angiotensin II engages different pathways when regulating insulin receptor interactions with IRS1 and IRS4. Angiotensin II inhibited the interaction between insulin receptor and IRS1 through activation of ERK1/2, while the interaction between insulin receptor and IRS4 was partially inhibited through protein kinase C dependent mechanisms. We conclude that the crosstalk between angiotensin AT₁ receptor and insulin receptor signaling shows a high degree of specificity, and involves Gαq protein, and activation of distinct kinases. Thus, the BRET² technique can be used as a platform for studying molecular mechanisms of crosstalk between insulin receptor and 7TM receptors.     

Gauging megadiversity with optimized and standardized sampling protocols: A case for tropical forest spiders

Characterizing and monitoring biodiversity and assessing its drivers require accurate and comparable data on species assemblages, which, in turn, should rely on efficient and standardized field collection. Unfortunately, protocols that follow such criteria remain scarce and it is unclear whether they can be applied to megadiverse communities, whose study can be particularly challenging. Here, we develop and evaluate the first optimized and standardized sampling protocol for megadiverse communities, using tropical forest spiders as a model taxon. We designed the protocol COBRA‐TF (Conservation Oriented Biodiversity Rapid Assessment for Tropical Forests) using a large dataset of semiquantitative field data from different continents. This protocol combines samples of different collecting methods to obtain as many species as possible with minimum effort (optimized) and widest applicability and comparability (standardized). We ran sampling simulations to assess the efficiency of COBRA‐TF (optimized, non‐site‐specific) and its reliability for estimating taxonomic, phylogenetic, and functional diversity, and community structure by comparing it with (1) commonly used expert‐based ad hoc protocols (nonoptimized, site‐specific) and (2) optimal protocols (optimized, site‐specific). We then tested the performance and feasibility of COBRA‐TF in the field. COBRA‐TF yielded similar results as ad hoc protocols for species (observed and estimated) and family richness, phylogenetic and functional diversity, and species abundance distribution. Optimal protocols detected more species than COBRA‐TF. Data from the field test showed high sampling completeness and yielded low numbers of singletons and doubletons. Optimized and standardized protocols can be as effective in sampling and studying megadiverse communities as traditional sampling, while allowing data comparison. Although our target taxa are spiders, COBRA‐TF can be modified to apply to any highly diverse taxon and habitat as long as multiple collecting techniques exist and the unit effort per sample is comparable. Protocols such as COBRA‐TF facilitate studying megadiverse communities and therefore may become essential tools for monitoring community changes in space and time, assessing the effects of disturbances and selecting conservation areas.     

Rounding up the usual suspects: a standard target‐gene approach for resolving the interfamilial phylogenetic relationships of ecribellate orb‐weaving spiders with a new family‐rank classification (Araneae,Araneoidea)

We test the limits of the spider superfamily Araneoidea and reconstruct its interfamilial relationships using standard molecular markers. The taxon sample (363 terminals) comprises for the first time representatives of all araneoid families, including the first molecular data of the family Synaphridae. We use the resulting phylogenetic framework to study web evolution in araneoids. Araneoidea is monophyletic and sister to Nicodamoidea rank. n. Orbiculariae are not monophyletic and also include the RTA clade, Oecobiidae and Hersiliidae. Deinopoidea is paraphyletic with respect to a lineage that includes the RTA clade, Hersiliidae and Oecobiidae. The cribellate orb‐weaving family Uloboridae is monophyletic and is sister group to a lineage that includes the RTA Clade, Hersiliidae and Oecobiidae. The monophyly of most Araneoidea families is well supported, with a few exceptions. Anapidae includes holarchaeids but the family remains diphyletic even if Holarchaea is considered an anapid. The orb‐web is ancient, having evolved by the early Jurassic; a single origin of the orb with multiple “losses” is implied by our analyses. By the late Jurassic, the orb‐web had already been transformed into different architectures, but the ancestors of the RTA clade probably built orb‐webs. We also find further support for a single origin of the cribellum and multiple independent losses. The following taxonomic and nomenclatural changes are proposed: the cribellate and ecribellate nicodamids are grouped in the superfamily Nicodamoidea rank n. (Megadictynidae rank res. and Nicodamidae stat. n. ). Araneoidea includes 17 families with the following changes: Araneidae is re‐circumscribed to include nephilines , Nephilinae rank res., Arkyidae rank n. , Physoglenidae rank n. , Synotaxidae is limited to the genus Synotaxus, Pararchaeidae is a junior synonym of Malkaridae ( syn. n. ), Holarchaeidae of Anapidae ( syn. n. ) and Sinopimoidae of Linyphiidae ( syn. n. ).