Assessment of sex-specific effects in a genome-wide association study of rheumatoid arthritis

Rheumatoid arthritis (RA) is three times more common in females than in males, suggesting that sex may play a role in modifying genetic associations with disease. We have addressed this hypothesis by performing sex-differentiated and sex-interaction analyses of a genome-wide association study of RA in a North American population. Our results identify a number of novel associations that demonstrate strong evidence of association in both sexes combined, with no evidence of heterogeneity in risk between males and females. However, our analyses also highlight a number of associations with RA in males or females only. These signals may represent true sex-specific effects, or may reflect a lack of power to detect association in the smaller sample of males, and thus warrant further investigation

A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform

<p>Abstract</p> <p>Background</p> <p>The 27k Illumina Infinium Methylation Beadchip is a popular high-throughput technology that allows the methylation state of over 27,000 CpGs to be assayed. While feature selection and classification methods have been comprehensively explored in the context of gene expression data, relatively little is known as to how best to perform feature selection or classification in the context of Illumina Infinium methylation data. Given the rising importance of epigenomics in cancer and other complex genetic diseases, and in view of the upcoming epigenome wide association studies, it is critical to identify the statistical methods that offer improved inference in this novel context.</p> <p>Results</p> <p>Using a total of 7 large Illumina Infinium 27k Methylation data sets, encompassing over 1,000 samples from a wide range of tissues, we here provide an evaluation of popular feature selection, dimensional reduction and classification methods on DNA methylation data. Specifically, we evaluate the effects of variance filtering, supervised principal components (SPCA) and the choice of DNA methylation quantification measure on downstream statistical inference. We show that for relatively large sample sizes feature selection using test statistics is similar for M and β-values, but that in the limit of small sample sizes, M-values allow more reliable identification of true positives. We also show that the effect of variance filtering on feature selection is study-specific and dependent on the phenotype of interest and tissue type profiled. Specifically, we find that variance filtering improves the detection of true positives in studies with large effect sizes, but that it may lead to worse performance in studies with smaller yet significant effect sizes. In contrast, supervised principal components improves the statistical power, especially in studies with small effect sizes. We also demonstrate that classification using the Elastic Net and Support Vector Machine (SVM) clearly outperforms competing methods like LASSO and SPCA. Finally, in unsupervised modelling of cancer diagnosis, we find that non-negative matrix factorisation (NMF) clearly outperforms principal components analysis.</p> <p>Conclusions</p> <p>Our results highlight the importance of tailoring the feature selection and classification methodology to the sample size and biological context of the DNA methylation study. The Elastic Net emerges as a powerful classification algorithm for large-scale DNA methylation studies, while NMF does well in the unsupervised context. The insights presented here will be useful to any study embarking on large-scale DNA methylation profiling using Illumina Infinium beadarrays.</p

Did China's Foreign Exchange Policy Hinder the US Recovery from the Global Financial Crisis?

...substantially undervalued...” - Tim Geithner, US Treasury, January 2011 “...China manipulates its currency...” - Charles Schumer (D), February 2011 “...huge competitive disadvantage...” - President Obama, February 2010 The quotes above convey the perception that China’s foreign exchange policy has had a harmful impact on the US economy. This paper examines whether China’s foreign exchange policy harmed the US economy wit h particular reference to its GDP and unemployment levels since the onset of the GF C. We find, contrary to the commonly held belief, that China’s foreign exchange policy has in fact helped the US recover from the GFC, albeit at the cost of strategi c dependency on Chinese demand for its government debt

Combination of a mitogen‐activated protein kinase inhibitor with the tyrosine kinase inhibitor pacritinib combats cell adhesion‐based residual disease and prevents re‐expansion of FLT3 ‐ITD acute myeloid leukaemia

Minimal residual disease (MRD) in acute myeloid leukaemia (AML) poses a major challenge due to drug insensitivity and high risk of relapse. Intensification of chemotherapy and stem cell transplantation are often pivoted on MRD status. Relapse rates are high even with the integration of first‐generation FMS‐like tyrosine kinase 3 (FLT3) inhibitors in pre‐ and post‐transplant regimes and as maintenance in FLT3 ‐mutated AML. Pre‐clinical progress is hampered by the lack of suitable modelling of residual disease and post‐therapy relapse. In the present study, we investigated the nature of pro‐survival signalling in primary residual tyrosine kinase inhibitor (TKI)‐treated AML cells adherent to stroma and further determined their drug sensitivity in order to inform rational future therapy combinations. Using a primary human leukaemia‐human stroma model to mimic the cell–cell interactions occurring in patients, the ability of several TKIs in clinical use, to abrogate stroma‐driven leukaemic signalling was determined, and a synergistic combination with a mitogen‐activated protein kinase (MEK) inhibitor identified for potential therapeutic application in the MRD setting. The findings reveal a common mechanism of stroma‐mediated resistance that may be independent of mutational status but can be targeted through rational drug design, to eradicate MRD and reduce treatment‐related toxicity

Evaluation and monitoring of terrestrial and aquatic insect biodiversity in forested and cleared watersheds at Camp Atterbury, Indiana.

Executive Summary Camp Atterbury is a 33,132 ha military installation near Edinburgh, Indiana. Construction of a 80 ha (4,550 ha with safety fan) Multi-Purpose Training Range (MPTR) began in 1998, and supports training for military vehicles and dismounted infantry, with a variety of stationary and moving targets. This study provides a baseline for long term monitoring and evaluation of natural communities to assess the impacts of construction of, and training in, the MPTR. We assessed both aquatic macroinvertebrate and terrestrial insect community diversity, abundance, and richness and similarity at a series of study plots using quantifiable, repeatable and replicated methods. These data provide baseline data facilitating long-term monitoring and assessment as a measure of ecosystem health, and allow evaluation of relationships between community composition and habitat metrics. Methods Eight terrestrial study sites, each comprised of a 30 m square plot, were randomly selected, with four of these placed in the cleared portions of the MPTR and four placed in adjacent upland forest. We used several sampling methods, with focus on three groups of taxa (all insect taxa, ants, and leafhoppers and kin) and compared the efficacy of both the methods and the groups as monitoring tools. Sampling methods included: 1) a Malaise trap (mesh tent-like device that captures flying insects) at each site; 2) four sweep sample transects at each site; 3) four leaf litter samples from each site, with invertebrates extracted using the Winkler method; and 4) Nine pitfall traps at each site. Samples were collect during Summer and Fall study periods, and this report gives results from the Summer sample period. Several habitat parameters were recorded, including a vegetation index, canopy cover, ground cover, and leaf litter depth. Dominant plant taxa were collected, and data loggers recorded soil and air temperature during the study. We sampled aquatic macroinvertebrates at three stream sites draining the MPTR. Invertebrates were collected in replicate samples with a dipnet and these were sorted and subsampled in the laboratory. Canopy cover and basic water chemistry data were collected, and data loggers recorded changes in terrestrial and aquatic temperature. An index of biotic integrity and taxon richness were used to evaluate the aquatic communities. Results and Discussion At least 409 taxa and 3776 specimens were collected at terrestrial sample sites during the Summer sampling period. In general, there were some differences among sites, among sampling methods, and among treatments (cleared MPTR versus forested) when we examined taxon richness and species diversity, but these differences could not always be fully resolved. While taxon richness and species diversity differed among treatments, and, in general, plots in the two treatments harbored different insect communities. Species accumulation curves and various estimators of taxon richness were used to evaluate the four sampling methods and the three groups of taxa (all taxa, ants, leafhoppers). Based on the performance of the different taxa (all, ants, leafhoppers) compared across the different methods (malaise sampling, Winkler extracted leaf litter samples, pitfall traps, and sweep samples), the single most effective taxon for monitoring was found to be the ants (Formicidae), and the single best method for monitoring was found to be pitfall trapping. We collected 818 specimens, primarily aquatic macroinvertebrates, from the three stream sites during Summer sampling. All three streams were dry during the fall sample period, and thus no aquatic macroinvertebrates were collected. Using Hilsenhoff’s (1988) family-level index of biotic integrity, water quality was classified as “good” at one site, and “fair” at the other two, although taxon richness was lowest at the site classified as good. In addition to invertebrates, numerous salamanders (Eurycea cirrigera, the Two-lined Salamander) were observed in the streams. 3 For aquatic invertebrates, we found that the small upstream portions that directly drained the MPTR only held water seasonally, and thus were not effective sites for monitoring of stream macroinvertebrates. There was insufficient separation between MPTR-influenced stream sites and control sites, and a lack of replication (few streams flowing away from the MPTR) precluded robust statistical analysis of the data we did obtain. The community of aquatic macroinvertebrates collected during this study appeared similar to the communities reported by Robinson (2004) elsewhere at Camp Atterbury in larger streams, and includes taxa typical of rocky bottom Midwestern forest streams. Fish were largely absent due to the intermittent nature of the streams. Salamanders were abundant in the streams, and because they are top predators in this seasonal habitat, they may be suitable subjects for studies of potential bioaccumulation of toxins. This study provides a snapshot of insect biodiversity at a point in time, thus providing baseline for any possible future monitoring of insect biodiversity. Sampling methods and analyses developed in this study could easily be implemented at a wide variety of other military installations to facilitate inventory and/or monitoring of insect biodiversity.Ope

A dual role for SAMHD1 in regulating HBV cccDNA and RT-dependent particle genesis

Chronic hepatitis B is one of the world's unconquered diseases with more than 240 million infected subjects at risk of developing liver disease and hepatocellular carcinoma. Hepatitis B virus reverse transcribes pre-genomic RNA to relaxed circular DNA (rcDNA) that comprises the infectious particle. To establish infection of a naïve target cell, the newly imported rcDNA is repaired by host enzymes to generate covalently closed circular DNA (cccDNA), which forms the transcriptional template for viral replication. SAMHD1 is a component of the innate immune system that regulates deoxyribonucleoside triphosphate levels required for host and viral DNA synthesis. Here, we show a positive role for SAMHD1 in regulating cccDNA formation, where KO of SAMHD1 significantly reduces cccDNA levels that was reversed by expressing wild-type but not a mutated SAMHD1 lacking the nuclear localization signal. The limited pool of cccDNA in infected Samhd1 KO cells is transcriptionally active, and we observed a 10-fold increase in newly synthesized rcDNA-containing particles, demonstrating a dual role for SAMHD1 to both facilitate cccDNA genesis and to restrict reverse transcriptase-dependent particle genesis

Lrp5 Is Not Required for the Proliferative Response of Osteoblasts to Strain but Regulates Proliferation and Apoptosis in a Cell Autonomous Manner

Although Lrp5 is known to be an important contributor to the mechanisms regulating bone mass, its precise role remains unclear. The aim of this study was to establish whether mutations in Lrp5 are associated with differences in the growth and/or apoptosis of osteoblast-like cells and their proliferative response to mechanical strain in vitro. Primary osteoblast-like cells were derived from cortical bone of adult mice lacking functional Lrp5 (Lrp5−/−), those heterozygous for the human G171V High Bone Mass (HBM) mutation (LRP5G171V) and their WT littermates (WTLrp5, WTHBM). Osteoblast proliferation over time was significantly higher in cultures of cells from LRP5G171V mice compared to their WTHBM littermates, and lower in Lrp5−/− cells. Cells from female LRP5G171V mice grew more rapidly than those from males, whereas cells from female Lrp5−/− mice grew more slowly than those from males. Apoptosis induced by serum withdrawal was significantly higher in cultures from Lrp5−/− mice than in those from WTHBM or LRP5G171V mice. Exposure to a single short period of dynamic mechanical strain was associated with a significant increase in cell number but this response was unaffected by genotype which also did not change the ‘threshold’ at which cells responded to strain. In conclusion, the data presented here suggest that Lrp5 loss and gain of function mutations result in cell-autonomous alterations in osteoblast proliferation and apoptosis but do not alter the proliferative response of osteoblasts to mechanical strain in vitro

Characteristics of Stem Cells Derived from the Degenerated Human Intervertebral Disc Cartilage Endplate

Mesenchymal stem cells (MSCs) derived from adult tissues are an important candidate for cell-based therapies and regenerative medicine due to their multipotential differentiation capability. MSCs have been identified in many adult tissues but have not reported in the human intervertebral disc cartilage endplate (CEP). The initial purpose of this study was to determine whether MSCs exist in the degenerated human CEP. Next, the morphology, proliferation capacity, cell cycle, cell surface epitope profile and differentiation capacity of these CEP-derived stem cells (CESCs) were compared with bone-marrow MSCs (BM-MSCs). Lastly, whether CESCs are a suitable candidate for BM-MSCs was evaluated. Isolated cells from degenerated human CEP were seeded in an agarose suspension culture system to screen the proliferative cell clusters. Cell clusters were chosen and expanded in vitro and were compared with BM-MSCs derived from the same patient. The morphology, proliferation rate, cell cycle, immunophenotype and stem cell gene expression of the CESCs were similar to BM-MSCs. In addition, the CESCs could be induced into osteoblasts, adipocytes, chondrocytes, and are superior to BM-MSCs in terms of osteogenesis and chondrogenesis. This study is first to demonstrate the presence of stem cells in the human degenerated CEP. These results may improve our understanding of intervertebral disc (IVD) pathophysiology and the degeneration process, and could provide cell candidates for cell-based regenerative medicine and tissue engineering

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead