Identification of oscillatory genes in somitogenesis from functional genomic analysis of a human mesenchymal stem cell model

During somitogenesis, oscillatory expression of genes in the notch and wnt signaling pathways plays a key role in regulating segmentation. These oscillations in expression levels are elements of a species-specific developmental mechanism. To date, the periodicity and components of the human clock remain unstudied. Here we show that a human mesenchymal stem/stromal cell (MSC) model can be induced to display oscillatory gene expression. We observed that the known cycling gene HES1 oscillated with a 5 h period consistent with available data on the rate of somitogenesis in humans. We also observed cycling of Hes1 expression in mouse C2C12 myoblasts with a period of 2 h, consistent with previous in vitro and embryonic studies. Furthermore, we used microarray and quantitative PCR (Q-PCR) analysis to identify additional genes that display oscillatory expression both in vitro and in mouse embryos. We confirmed oscillatory expression of the notch pathway gene Maml3 and the wnt pathway gene Nkd2 by whole mount in situ hybridization analysis and Q-PCR. Expression patterns of these genes were disrupted in Wnt3a(tm1Amc) mutants but not in Dll3(pu) mutants. Our results demonstrate that human and mouse in vitro models can recapitulate oscillatory expression observed in embryo and that a number of genes in multiple developmental pathways display dynamic expression in vitro.     

Alanine Scanning Studies of the Antimicrobial Peptide Aurein 1.2

Antimicrobial peptides (AMPs) are compounds widely distributed in nature that display activity against a broad spectrum of pathogens. Amphibian skin, as an organ rich in pharmacologically active peptides, appears to be an interesting source of novel AMPs. Aurein 1.2 (GLFDIIKKIAESF-NH₂) is a short 13-residue antimicrobial peptide primarily isolated from the skin secretions of Australian bell frogs. In this study, the alanine scan of aurein 1.2 was performed to investigate the effect of each amino acid residue on its biological and physico-chemical properties. The biological studies included determination of minimum inhibitory concentration, activity against biofilm, and inhibitory effect on its formation. Moreover, the hemolytic activity as well as serum stability was determined. The hydrophobicity of peptides and their self-assembly were investigated using reversed-phase chromatography. In addition, their helicity was calculated from circular dichroism spectra. The results not only provided information on structure-activity relationship of aurein 1.2 but also gave insights into design of novel analogs of AMPs in the future.

     

QTLs associated with dry matter intake,metabolic mid-test weight,growth and feed efficiency have little overlap across 4 beef cattle studies

Background

The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental × Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake.

Results

A total of 5, 6, 11 and 10 significant QTL (defined as 1-Mb genome windows with Bonferroni-corrected P-value <0.05) were identified for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake, respectively. The identified QTL were population-specific and had little overlap across the 4 populations. The pleiotropic or closely linked QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with dry matter intake and mid-test body weight explaining 10.39% and 14.25% of the additive genetic variance, respectively. Pleiotropic or closely linked QTL associated with average daily gain and mid-test body weight were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for residual feed intake explained more than 2.5% of the additive genetic variance in any population. Marker-based estimates of heritability ranged from 0.21 to 0.49 for residual feed intake across the 4 populations.

Conclusions

This GWAS study, which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained a significant percentage of additive genetic variance within each population. Differences in the QTL identified among the different populations may be due to differences in power to detect QTL, environmental variation, or differences in the genetic architecture of trait variation among breeds. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.     

Recombination locations and rates in beef cattle assessed from parent-offspring pairs

Background

Recombination events tend to occur in hotspots and vary in number among individuals. The presence of recombination influences the accuracy of haplotype phasing and the imputation of missing genotypes. Genes that influence genome-wide recombination rate have been discovered in mammals, yeast, and plants. Our aim was to investigate the influence of recombination on haplotype phasing, locate recombination hotspots, scan the genome for Quantitative Trait Loci (QTL) and identify candidate genes that influence recombination, and quantify the impact of recombination on the accuracy of genotype imputation in beef cattle.

Methods

2775 Angus and 1485 Limousin parent-verified sire/offspring pairs were genotyped with the Illumina BovineSNP50 chip. Haplotype phasing was performed with DAGPHASE and BEAGLE using UMD3.1 assembly SNP (single nucleotide polymorphism) coordinates. Recombination events were detected by comparing the two reconstructed chromosomal haplotypes inherited by each offspring with those of their sires. Expected crossover probabilities were estimated assuming no interference and a binomial distribution for the frequency of crossovers. The BayesB approach for genome-wide association analysis implemented in the GenSel software was used to identify genomic regions harboring QTL with large effects on recombination. BEAGLE was used to impute Angus genotypes from a 7K subset to the 50K chip.

Results

DAGPHASE was superior to BEAGLE in haplotype phasing, which indicates that linkage information from relatives can improve its accuracy. The estimated genetic length of the 29 bovine autosomes was 3097 cM, with a genome-wide recombination distance averaging 1.23 cM/Mb. 427 and 348 windows containing recombination hotspots were detected in Angus and Limousin, respectively, of which 166 were in common. Several significant SNPs and candidate genes, which influence genome-wide recombination were localized in QTL regions detected in the two breeds. High-recombination rates hinder the accuracy of haplotype phasing and genotype imputation.

Conclusions

Small population sizes, inadequate half-sib family sizes, recombination, gene conversion, genotyping errors, and map errors reduce the accuracy of haplotype phasing and genotype imputation. Candidate regions associated with recombination were identified in both breeds. Recombination analysis may improve the accuracy of haplotype phasing and genotype imputation from low- to high-density SNP panels.     

Molecular Anatomy and Number of Antigen Specific CD8 T Cells Required to Cause Type 1 Diabetes

We quantified CD8 T cells needed to cause type 1 diabetes and studied the anatomy of the CD8 T cell/beta (β) cell interaction at the immunologic synapse. We used a transgenic model, in situ tetramer staining to distinguish antigen specific CD8 T cells from total T cells infiltrating islets and a variety of viral mutants selected for functional deletion(s) of various CD8 T cell epitopes. Twenty percent of CD8 T cells in the spleen were specific for all immunodominant and subdominant viral glycoprotein (GP) epitopes. CTLs to the immunodominant LCMV GP33-41 epitope accounted for 63% of the total (12.5% of tetramers). In situ hybridization analysis demonstrated only 1 to 2% of total infiltrating CD8 T cells were specific for GP33 CD8 T cell epitope, yet diabetes occurred in 94% of mice. The immunologic synapse between GP33 CD8 CTL and β cell contained LFA-1 and perforin. Silencing both immunodominant epitopes (GP33, GP276–286) in the infecting virus led to a four-fold reduction in viral specific CD8 CTL responses, negligible lymphocyte infiltration into islets and absence of diabetes.     

Molecular and cellular biology of neuroendocrine lung tumors: Evidence for separate biological entities

Pulmonary neuroendocrine tumors (NETs) are traditionally described as comprising a spectrum of neoplasms, ranging from low grade typical carcinoids (TCs) via the intermediate grade atypical carcinoids (ACs) to the highly malignant small cell lung cancers (SCLCs) and large cell neuroendocrine carcinomas (LCNECs). Recent data, however, suggests that two categories can be distinguished on basis of molecular and clinical data, i.e. the high grade neuroendocrine (NE) carcinomas and the carcinoid tumors. Bronchial carcinoids and SCLCs may originate from the same pulmonary NE precursor cells, but a precursor lesion has only been observed in association with carcinoids, termed diffuse idiopathic pulmonary neuroendocrine cell hyperplasia. The occurrence of mixed tumors exclusively comprising high grade NE carcinomas also supports a different carcinogenesis for these two groups. Histopathologically, high grade NE lung tumors are characterized by high mitotic and proliferative indices, while carcinoids are defined by maximally 10 mitoses per 2mm(2) (10 high-power fields) and rarely have Ki67-proliferative indices over 10%. High grade NE carcinomas are chemosensitive tumors, although they usually relapse. Surgery is often not an option due to extensive disease at presentation and early metastasis, especially in SCLC. Conversely, carcinoids are often insensitive to chemo- and radiation therapy, but cure can usually be achieved by surgery. A meta-analysis of comparative genomic hybridization studies performed for this review, as well as gene expression profiling data indicates separate clustering of carcinoids and carcinomas. Chromosomal aberrations are much more frequent in carcinomas, except for deletion of 11q, which is involved in the whole spectrum of NE lung tumors. Deletions of chromosome 3p are rare in carcinoids but are a hallmark of the high grade pulmonary NE carcinomas. On the contrary, mutations of the multiple endocrine neoplasia type 1 (MEN1) gene are restricted to carcinoid tumors. Many of the differences between carcinoids and high grade lung NETs can be ascribed to tobacco consumption, which is strongly linked to the occurrence of high grade NE carcinomas. Smoking causes p53 mutations, very frequently present in SCLCs and LCNECs, but rarely in carcinoids. It further results in other early genetic events in SCLCs and LCNECs, such as 3p and 17p deletions. Smoking induces downregulation of E-cadherin and associated epithelial to mesenchymal transition. Also, high grade lung NETs display higher frequencies of aberrations of the Rb pathway, and of the intrinsic and extrinsic apoptotic routes. Carcinoid biology on the other hand is not depending on cigarette smoke intake but rather characterized by aberrations of other specific genetic events, probably including Menin or its targets and interaction partners. This results in a gradual evolution, most likely from proliferating pulmonary NE cells via hyperplasia and tumorlets towards classical carcinoid tumors. We conclude that carcinoids and high grade NE lung carcinomas are separate biological entities and do not comprise one spectrum of pulmonary NETs. This implies the need to reconsider both diagnostic as well as therapeutic approaches for these different groups of malignancies.     

The 1.8-A crystal structure of alpha1-acid glycoprotein (Orosomucoid) solved by UV RIP reveals the broad drug-binding activity of this human plasma lipocalin

α₁-Acid glycoprotein (AGP) is an important drug-binding protein in human plasma and, as an acute-phase protein, it has a strong influence on pharmacokinetics and pharmacodynamics of many pharmaceuticals. We report the crystal structure of the recombinant unglycosylated human AGP at 1.8 Å resolution, which was solved using the new method of UV-radiation-damage-induced phasing (UV RIP). AGP reveals a typical lipocalin fold comprising an eight-stranded β-barrel. Of the four loops that form the entrance to the ligand-binding site, loop 1, which connects β-strands A and B, is among the longest observed so far and exhibits two full turns of an α-helix. Furthermore, it carries one of the five N-linked glycosylation sites, while a second one occurs underneath the tip of loop 2. The branched, partly hydrophobic, and partly acidic cavity, together with the presumably flexible loop 1 and the two sugar side chains at its entrance, explains the diverse ligand spectrum of AGP, which is known to vary with changes in glycosylation pattern.     

Fish-oil supplementation in patients with implantable cardioverter defibrillators: a meta-analysis

Background

A recent Cochrane meta-analysis did not confirm the benefits of fish and fish oil in the secondary prevention of cardiac death and myocardial infarction. We performed a meta-analysis of randomized controlled trials that examined the effect of fish-oil supplementation on ventricular fibrillation and ventricular tachycardia to determine the overall effect and to assess whether heterogeneity exists between trials.

Methods

We searched electronic databases (MEDLINE, EMBASE, The Cochrane Central Register of Controlled Trials, CINAHL) from inception to May 2007. We included randomized controlled trials of fish-oil supplementation on ventricular fibrillation or ventricular tachycardia in patients with implantable cardioverter defibrillators. The primary outcome was implantable cardioverter defibrillator discharge. We calculated relative risk [RR] for outcomes at 1-year follow-up for each study. We used the DerSimonian and Laird random-effects methods when there was significant heterogeneity between trials and the Mantel-Hanzel fixed-effects method when heterogeneity was negligible.

Results

We identified 3 trials of 1–2 years'' duration. These trials included a total of 573 patients who received fish oil and 575 patients who received a control. Meta-analysis of data collected at 1 year showed no overall effect of fish oil on the relative risk of implantable cardioverter defibrillator discharge. There was significant heterogeneity between trials. The second largest study showed a significant benefit of fish oil (relative risk [RR] 0.74, 95% confidence interval [CI] 0.56–0.98). The smallest showed an adverse tendency at 1 year (RR 1.23, 95% CI 0.92–1.65) and significantly worse outcome at 2 years among patients with ventricular tachycardia at study entry (log rank p = 0.007).

Conclusion

These data indicate that there is heterogeneity in the response of patients to fish-oil supplementation. Caution should be used when prescribing fish-oil supplementation for patients with ventricular tachycardia.There is a public perception that fish and fish oil can be recommended uniformly for the prevention of coronary artery disease.^1–3 However, the scientific evidence is divided^4,5 and official agencies have called for more research.⁶It is estimated that 0.5% of patients with coronary heart disease, 1% of patients with diabetes or hypertension and 2% of the general population at low risk of coronary heart disease take fish-oil supplements.⁷ In 2004, the price of fish oils overtook that of vegetable oils, and in 2006, the price rose to US$750 per ton.⁸ The value of fish oil as a nutraceutical in the European market was US$194 million in 2004, and it is anticipated that the price will continue to rise as availability declines.⁸ Canada is both a consumer and an exporter of fish oil, and it exported 15 000 tons in 2006.⁹The scientific debate over the clinical value of fish oil is highlighted by a recent Cochrane review, which concluded that long-chain omega-3 fatty acids (eicosapentaenoic acid and docosahexaenoic acid) had no clear effect on total mortality, combined cardiovascular events or cancer.⁴ Furthermore, another recent meta-analysis¹⁰ only showed a significant positive association between fish-oil consumption and prevention of restenosis after coronary angioplasty in a select subgroup after excluding key negative papers.¹¹ Finally, the antiarrhythmic effect, which is proposed to be the principal mechanism of their benefit in cardiovascular disease, has not been demonstrated clearly in clinical trials.^12–14We therefore performed a meta-analysis of randomized controlled trials that examined the effect of fish-oil supplementation in patients with implantable cardioverter defibrillators who are at risk of ventricular arrhythmia to determine the overall effect of fish oils. We also sought to investigate whether there was significant heterogeneity between trials.     

Selective serotonin reuptake inhibitors for unipolar depression: a systematic review of classic long-term randomized controlled trials

Background

Selective serotonin reuptake inhibitors are increasingly used in the long-term treatment of depression. Much of the supporting evidence about the effects of these drugs comes from discontinuation trials, a variant of randomized controlled trials whose design is problematic to interpret. We conducted a systematic review to examine the efficacy and acceptability of long-term therapy with selective serotonin reuptake inhibitors relative to placebo in the treatment of unipolar depression.

Methods

We identified placebo-controlled randomized trials with a treatment duration of at least 6 months by searching MEDLINE, EMBASE and the Cochrane Central Register of Controlled Trials to update a recently published systematic review. Efficacy was defined in terms of response to treatment (50% improvement in depression score relative to baseline) and remission (score of 7 or below on the Hamilton rating scale for depression). Key secondary outcomes included quality of life, return to work, need for additional treatment and self-harm. Overall acceptability was defined in terms of dropouts for any reason over a course of treatment.

Results

Of the 2693 records identified initially, we included 6 randomized controlled trials that met our eligibility criteria. These studies had a moderate risk of bias, had assigned a total of 1299 participants with depression to either treatment or placebo and had followed both groups for 6–8 months. We observed statistically significant improvements in response to treatment (odds ratio [OR] 1.66, 95% confidence interval [CI] 1.12–2.48), but not in remission (OR 1.46, 95% CI 0.92–2.32) or acceptability (OR 0.87, 95% CI 0.67–1.14). The effects appeared greater among patients without comorbidities.

Interpretation

There is a lack of classic randomized controlled trials of serotonin reuptake inhibitors lasting more than 1 year for the treatment of depression. The results of our systematic review support current recommendations for 6–8 months of antidepressant treatment following initial recovery but provide no guidance for longer treatment.Over the past decade, the use of selective serotonin reuptake inhibitors for the management of depression has increased dramatically, and preliminary evidence suggests that long-term use, for more than 1 or 2 years, accounts for much of this rise.^1–3 Clinical practice guidelines generally recommend a 6- to 9-month course following initial recovery after a first episode of depression and longer, sometimes indefinite, therapy after subsequent episodes, to prevent relapse.^4–10Long-term randomized controlled trials of antidepressants have typically used 1 of 2 possible designs, each answering different questions (Figure 1).¹¹ The most widely used design is called the “discontinuation trial,” a 2-phase study in which all participants are initially treated with an open (unblinded) course of drug therapy. Participants attaining a certain response during the open-treatment phase enter the second phase, during which they are randomly assigned to continue active drug treatment or to receive placebo.^12–14 Discontinuation trials are believed to minimize the number of participants with depression who must be exposed to placebo. This advantage comes at a cost, since the results apply only to patients with a response to the medication, not to those who experience spontaneous recovery; furthermore, withdrawal symptoms may lead to an overestimate of the true effect of the medication. When this design is used to test long-term therapy with selective serotonin reuptake inhibitors for the treatment of depression, the results are difficult to interpret with confidence because rates of spontaneous recovery in depression are potentially high and because withdrawal effects can mimic depression.^13–15Open in a separate windowFigure 1: Two designs of randomized controlled trials used to investigate long-term antidepressant therapy.The second type of randomized trial used to test long-term therapy with selective serotonin reuptake inhibitors is a 2-arm parallel randomized controlled trial, hereafter referred to as a classic randomized controlled trial (Figure 1).¹⁶ In this type of trial, participants with acute depression are assigned to receive either placebo or active drug, and all those achieving a certain response, either to the drug or to the placebo, are followed. The advantage of classic randomized controlled trials is that data from all participants contribute to our understanding of the drug''s real-world effectiveness. Their main drawback is that a greater number of acutely ill people may have to receive placebo than in a discontinuation trial.¹³ Most classic trials of antidepressants are short-term studies. Fergusson and colleagues,¹⁷ in a systematic review examining selective serotonin reuptake inhibitors and suicide, identified 702 classic trials involving a total of 18 413 participants, the majority of which (93%) lasted less than 6 months.A recent systematic review based mainly on studies with discontinuation designs showed that, in a subgroup of patients who experienced recovery while taking medications, long-term therapy with selective serotonin reuptake inhibitors reduced the chances of relapse by up to 70% for up to 36 months, relative to patients whose therapy was discontinued earlier.⁶ However, there has been no systematic review of classic randomized trials of long-term therapy with this drug class to determine the potential benefits in all patients with depression, including those with spontaneous recovery.We sought to examine the efficacy and acceptability of long-term therapy with selective serotonin reuptake inhibitors relative to placebo in the treatment of moderate to severe depression, including subgroups of patients with major chronic health conditions. We also examined a number of key indicators of the quality of evidence and its clinical importance.