High-resolution profiling of protein occupancy on polyadenylated RNA transcripts

A key prerequisite to understand how gene regulatory processes are controlled by the interplay of RNA-binding proteins (RBPs) and ribonucleoprotein complexes with RNAs is the generation of comprehensive high-resolution maps of protein-RNA interactions. Recent advances in next-generation sequencing technology accelerated the development of various crosslinking and immunoprecipitation (CLIP) approaches to broadly identify RNA regions contacted by RNA-binding proteins. However these methods only consider single RNA-binding proteins and their contact sites, irrespective of the overall cis-regulatory sequence space contacted by other RNA interacting factors. Here we describe the application of protein occupancy profiling, a novel approach that globally displays the RNA contact sites of the poly(A)+ RNA-bound proteome. Protein occupancy profiling enables the generation of transcriptome-wide maps of protein-RNA interactions on polyadenylated transcripts and narrows the sequence search space for transcript regions involved in cis-regulation of gene expression in response to internal or external stimuli, altered cellular programs or disease

Geographical variation of cerebrovascular disease in New York State: the correlation with income

BACKGROUND: Income is known to be associated with cerebrovascular disease; however, little is known about the more detailed relationship between cerebrovascular disease and income. We examined the hypothesis that the geographical distribution of cerebrovascular disease in New York State may be predicted by a nonlinear model using income as a surrogate socioeconomic risk factor. RESULTS: We used spatial clustering methods to identify areas with high and low prevalence of cerebrovascular disease at the ZIP code level after smoothing rates and correcting for edge effects; geographic locations of high and low clusters of cerebrovascular disease in New York State were identified with and without income adjustment. To examine effects of income, we calculated the excess number of cases using a non-linear regression with cerebrovascular disease rates taken as the dependent variable and income and income squared taken as independent variables. The resulting regression equation was: excess rate = 32.075 - 1.22*10(-4)(income) + 8.068*10(-10)(income(2)), and both income and income squared variables were significant at the 0.01 level. When income was included as a covariate in the non-linear regression, the number and size of clusters of high cerebrovascular disease prevalence decreased. Some 87 ZIP codes exceeded the critical value of the local statistic yielding a relative risk of 1.2. The majority of low cerebrovascular disease prevalence geographic clusters disappeared when the non-linear income effect was included. For linear regression, the excess rate of cerebrovascular disease falls with income; each $10,000 increase in median income of each ZIP code resulted in an average reduction of 3.83 observed cases. The significant nonlinear effect indicates a lessening of this income effect with increasing income. CONCLUSION: Income is a non-linear predictor of excess cerebrovascular disease rates, with both low and high observed cerebrovascular disease rate areas associated with higher income. Income alone explains a significant amount of the geographical variance in cerebrovascular disease across New York State since both high and low clusters of cerebrovascular disease dissipate or disappear with income adjustment. Geographical modeling, including non-linear effects of income, may allow for better identification of other non-traditional risk factors

Immunomodulatory responses of peripheral blood mononuclear cells from multiple sclerosis patients upon in vitro incubation with the flavonoid luteolin: additive effects of IFN-β

The study is aimed to determine the role of luteolin (3',4',5,7-tetrahydroxyflavone), alone and in combination with human interferon-beta (IFN-β), in modulating the immune response(s) of peripheral blood mononuclear cells (PBMCs) isolated from multiple sclerosis (MS) patients. PBMC proliferation in the presence or absence of these drugs was determined and the production of pro-inflammatory cytokines (IL-1β, TNF-α), and the ratio of cell migration mediator MMP-9, and its inhibitor, TIMP-1 was assessed in the culture supernatants. Luteolin reduced, in a dose-dependent manner, the proliferation of PBMCs, and modulated the levels of IL-1β and TNF-α released by PBMCs in the culture supernatants. Luteolin reduced the MMP-9/TIMP-1 ratio via lowering MMP-9 production. In the majority of cases, luteolin, when combined with IFN-β, had additive effects in modulating cell proliferation, IL-1β, TNF-α, MMP-9 and TIMP-1

Comprehensive protein interactome analysis of a key RNA helicase: detection of novel stress granule proteins

DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. The screen is highly specific, maximizing the number of true positives, as demonstrated by the validation of 81% (47/58) of the RNA-independent interactors through known functions and interactions. Importantly, we minimize the number of indirect interaction partners through use of a nuclease-based digestion to eliminate RNA. We describe eleven new interactors, including proteins involved in splicing which is an as-yet unknown role for DDX6. We validated and characterized in more detail the interaction of DDX6 with Nuclear fragile X mental retardation-interacting protein 2 (NUFIP2) and with two previously uncharacterized proteins, FAM195A and FAM195B (here referred to as granulin-1 and granulin-2, or GRAN1 and GRAN2). We show that NUFIP2, GRAN1, and GRAN2 are not P-body components, but re-localize to stress granules upon exposure to stress, suggesting a function in translation repression in the cellular stress response. Using a complementary analysis that resolved DDX6's multiple complex memberships, we further validated these interaction partners and the presence of splicing factors. As DDX6 also interacts with the E3 SUMO ligase TIF1β, we tested for and observed a significant enrichment of sumoylation amongst DDX6's interaction partners. Our results represent the most comprehensive screen for direct interaction partners of a key regulator of RNA life cycle and localization, highlighting new stress granule components and possible DDX6 functions-many of which are likely conserved across eukaryotes

Diagnostic potential of plasma carboxymethyllysine and carboxyethyllysine in multiple sclerosis

<p>Abstract</p> <p>Background</p> <p>This study compared the level of advanced glycation end products (AGEs), <it>N</it>-(Carboxymethyl)lysine (CML) and <it>N</it>-(Carboxyethyl)lysine (CEL), in patients with multiple sclerosis (MS) and healthy controls (HCs), correlating these markers with clinical indicators of MS disease severity.</p> <p>Methods</p> <p>CML and CEL plasma levels were analyzed in 99 MS patients and 43 HCs by tandem mass spectrometry (LC/MS/MS). Patients were stratified based on drug modifying therapies (DMTs) including interferon beta, glatiramer acetate and natalizumab.</p> <p>Results</p> <p>The level of plasma CEL, but not CML, was significantly higher in DMT-naïve MS patients when compared to HCs (P < 0.001). Among MS patients, 91% had higher than mean plasma CEL observed in HCs. DMTs reduced CML and CEL plasma levels by approximately 13% and 40% respectively. CML and CEL plasma levels correlated with the rate of MS clinical relapse.</p> <p>Conclusion</p> <p>Our results suggest that AGEs in general and CEL in particular could be useful biomarkers in MS clinical practice. Longitudinal studies are warranted to determine any causal relationship between changes in plasma level of AGEs and MS disease pathology. These studies will pave the way for use of AGE inhibitors and AGE-breaking agents as new therapeutic modalities in MS.</p

Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat

Knockout of the ubiquitously expressed miRNA-17~92 cluster in mice produces a lethal developmental lung defect, skeletal abnormalities, and blocked B lymphopoiesis. A shared target of miR-17~92 miRNAs is the pro-apoptotic protein BIM, central to life-death decisions in mammalian cells. To clarify the contribution of miR-17~92:Bim interactions to the complex miR-17~92 knockout phenotype, we used a system of conditional mutagenesis of the nine Bim 3' UTR miR-17~92 seed matches. Blocking miR-17~92:Bim interactions early in development phenocopied the lethal lung phenotype of miR-17~92 ablation and generated a skeletal kinky tail. In the hematopoietic system, instead of causing the predicted B cell developmental block, it produced a selective inability of B cells to resist cellular stress; and prevented B and T cell hyperplasia caused by Bim haploinsufficiency. Thus, the interaction of miR-17~92 with a single target is essential for life, and BIM regulation by miRNAs serves as a rheostat controlling cell survival in specific physiological contexts

Effectiveness of systematic screening for the detection of atrial fibrillation

© 2013 The Cochrane Collaboration. Background: Atrial fibrillation (AF) is the most common arrhythmia in clinical practice and is a leading cause of morbidity and mortality. Screening for AF in asymptomatic patients has been proposed as a way of reducing the burden of the disease by detecting people who would benefit from prophylactic anticoagulation therapy prior to the onset of symptoms. However, for screening to be an effective intervention it must improve the detection of AF and provide benefit for those who are detected earlier as a result of screening. Objectives: The primary objective of this review was to examine whether screening programmes increase the detection of new cases of AF compared to routine practice. The secondary objectives were to identify which combination of screening strategy and patient population is most effective, as well as assessing any safety issues associated with screening, its acceptability within the target population and the costs involved. Search methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) on The Cochrane Library, MEDLINE (Ovid) and EMBASE (Ovid) up to March 2012. Other relevant research databases, trials registries and websites were searched up to June 2012. Reference lists of identified studies were also searched for potentially relevant studies and we contacted corresponding authors for information about additional published or unpublished studies that may be relevant. No language restrictions were applied. Selection criteria: Randomised controlled trials, controlled before and after studies and interrupted time series studies comparing screening for AF with routine practice in people aged 40 years and over were eligible. Two authors (PM, CT or MF) independently selected the trials for inclusion. Data collection and analysis: Assessment of risk of bias and data extraction were performed independently by two authors (PM, CT). Odds ratios (OR) and 95% confidence intervals (CI) were used to present the results for the primary outcome, which is a dichotomous variable. Since only one included study was identified, no meta-analysis was performed. Main results: One cluster randomised controlled trial met the inclusion criteria for this review. This study compared systematic screening (by invitation to have an electrocardiogram (ECG)) and opportunistic screening (pulse palpation during a general practitioner (GP) consultation for any reason followed by an ECG if pulse was irregular) to routine practice (normal case finding on the basis of clinical presentation) in people aged 65 years or older. The risk of bias in the included study was judged to be low. Both systematic and opportunistic screening of people over the age of 65 years are more effective than routine practice (OR 1.57, 95% CI 1.08 to 2.26 and OR 1.58, 95% CI 1.10 to 2.29, respectively). The number needed to screen in order to detect one additional case compared to routine practice was 172 (95% CI 94 to 927) for systematic screening and 167 (95% CI 92 to 806) for opportunistic screening. Both systematic and opportunistic screening were more effective in men (OR 2.68, 95% CI 1.51 to 4.76 and OR 2.33, 95% CI 1.29 to 4.19, respectively) than in women (OR 0.98, 95% CI 0.59 to 1.62 and OR 1.2, 95% CI 0.74 to 1.93, respectively). No data on the effectiveness of screening in different ethnic or socioeconomic groups were available. There were insufficient data to compare the effectiveness of screening programmes in different healthcare settings. Systematic screening was associated with a better overall uptake rate than opportunistic screening (53% versus 46%) except in the ≥ 75 years age group where uptake rates were similar (43% versus 42%). In both screening programmes men were more likely to participate than women (57% versus 50% in systematic screening, 49% versus 41% in opportunistic screening) and younger people (65 to 74 years) were more likely to participate than people aged 75 years and over (61% versus 43% systematic, 49% versus 42% opportunistic). No adverse events associated with screening were reported. The incremental cost per additional case detected by opportunistic screening was GBP 337, compared to GBP 1514 for systematic screening. All cost estimates were based on data from the single included trial, which was conducted in the UK between 2001 and 2003. Authors' conclusions: Systematic and opportunistic screening for AF increase the rate of detection of new cases compared with routine practice. While both approaches have a comparable effect on the overall AF diagnosis rate, the cost of systematic screening is significantly more than that of opportunistic screening from the perspective of the health service provider. The lack of studies investigating the effect of screening in other health systems and younger age groups means that caution needs to be exercised in relation to the transferability of these results beyond the setting and population in which the included study was conducted. Additional research is needed to examine the effectiveness of alternative screening strategies and to investigate the effect of the intervention on the risk of stroke for screened versus non-screened populations