Enforced expression of microRNA-155 (miR-155) in myeloid cells has been shown to have both oncogenic or tumour-suppressor functions in acute myeloid leukaemia (AML). We sought to resolve these ...contrasting effects of miR-155 overexpression using murine models of AML and human paediatric AML data sets. We show that the highest miR-155 expression levels inhibited proliferation in murine AML models. Over time, enforced miR-155 expression in AML in vitro and in vivo, however, favours selection of intermediate miR-155 expression levels that results in increased tumour burden in mice, without accelerating the onset of disease. Strikingly, we show that intermediate and high miR-155 expression also regulate very different subsets of miR-155 targets and have contrasting downstream effects on the transcriptional environments of AML cells, including genes involved in haematopoiesis and leukaemia. Furthermore, we show that elevated miR-155 expression detected in paediatric AML correlates with intermediate and not high miR-155 expression identified in our experimental models. These findings collectively describe a novel dose-dependent role for miR-155 in the regulation of AML, which may have important therapeutic implications.
An investigation of the spectral energy distribution (SED) of the compact steep-spectrum (CSS) source and possible radio-loud narrow-line Seyfert 1 galaxy (NLS1), PKS 2004-447, is presented. Five out ...of six well-studied radio-loud NLS1 share this dual classification optically defined as an NLS1 with radio definition of a CSS or gigahertz-peaked spectrum (GPS) source, suggesting that the connection could have a physical origin. The SED is created from simultaneous observations (within 24 h) at radio (from Australia Telescope Compact Array), optical/near-infrared (NIR) (from Siding Spring) and UV/X-ray (from XMM-Newton) wavelengths. The X-ray data show evidence of short-term variability (primarily a ∼30 per cent increase in the final 4 ks of the observation), a possible soft excess and negligible absorption. Together with the rest of the SED, the X-ray emission is excessive in comparison to synchrotron plus synchrotron self-Compton (SSC) models. The SED can be described with a two-component model consisting of extended synchrotron/SSC emission with Comptonization in the X-rays, though SSC models with a very high electron-to-magnetic energy density ratio cannot be excluded either. The peak emission in the SED appears to be in the NIR, which can be attributed to thermal emission (T≈ 1000 K) from a dusty torus. Analysis of a non-contemporaneous, low-resolution optical spectrum suggests that the narrow-line region (NLR) is much more reddened than the X-ray emitting region suggesting that the gas-to-dust ratio in PKS 2004-447 may be very different than in our own Galaxy. This could be achieved if the radio jets in PKS 2004-447 deposits material from the nucleus into the NLR. Long-term radio monitoring of PKS 2004-447 shows a rather constant light curve over nearly a six-month period with the exception of one outburst when the 6.65-GHz flux increased by ∼35 per cent over 19 d. It is not possible to differentiate between intrinsic or extrinsic (i.e. interstellar scintillation) origins for this outburst, but the detection of the rare event demonstrates the importance of intensive monitoring campaigns. In comparison to general samples of GPS sources, which appear to be X-ray weak, NLS1-CSS/GPS sources possess stronger X-ray emission relative to radio (comparable to normal radio-loud AGN). In addition, NLS1-CSS/GPS sources also exhibit lower intrinsic absorption than GPS sources of similar X-ray luminosity. This is consistent with the additional X-ray component required for PKS 2004-447, but larger samples of NLS1-CSS/GPS are needed before any conclusive remarks can be made.
BackgroundJuvenile idiopathic arthritis (JIA) is a paediatric autoimmune disease (AD) with a female preponderance, though this differs by subtype. Whether this sex bias is reflective of differing ...disease pathogenesis between the sexes is unknown. Gene expression signatures can be biologically and clinically informative, but few expression studies have been performed in JIA. Though gene expression is recognised as sexually dimorphic in many states, its role in JIA sex bias has not been considered. In response to infection females produce more antibodies than males, which could increase natural autoantibody production and the risk of developing AD. Gene expression differences between the sexes may reflect this. The reduced heterogeneity afforded by sex-stratified transcriptome-wide analysis may provide insight into how sex influences disease pathogenesis in JIA.ObjectivesWe aimed to identify sex-specific differences in patients with oligoarticular JIA versus healthy controls through RNA-seq analysis on CD4+ T cells.MethodsSix male and six female oligoarticular JIA cases, with no prior exposure to disease-modifying anti-rheumatic drugs, were age and sex-matched to healthy controls. CD4+ T cells were selected as existing data links T cell gene networks to JIA. RNA was extracted from CD4+ T cells using the Qiagen miRNeasy extraction kit. Sequencing library preparation was performed using the Illumina TruSeq Stranded Total RNA LT kit. One female sample did not pass quality control and was not sequenced. Sequencing was performed using 75bp paired-end reads to a depth of ∼20 million reads on the Illumina NextSeq. Quality trimmed reads were mapped to the genome using the STAR aligner. Read counts across exons and genes were summarised using featureCounts. Normalised read counts were used for differential gene expression analysis with edgeR. GOseq was used for gene ontology analysis. Males and females were analysed separately.ResultsNo sex-specific differentially expressed (DE) genes reached FDR adjusted p<0.05. At unadjusted p<0.05 there were far more male (1480) than female (118) specific DE genes, with 24 overlapping. Pathway analysis of male-specific DE genes highlighted antigen processing and presentation, immune response, and IFNΥ production, among other disease-relevant gene networks. Corresponding female-specific analysis did not reveal obvious disease-relevant networks. For many genes DE between male cases and controls, male case gene expression appeared more similar to all females (Figure 1).ConclusionsWe have identified sex-specific differences in CD4+ T cell gene expression between healthy controls and oligoarticular JIA cases predominantly in males, despite the female preponderance. Our data may reflect that some of the pathogenesis for JIA differs between the sexes, and that gene expression differences play a particularly important role in male JIA, perhaps by a more “female” immune response occurring in male cases. Given the small sample size, replication is necessary and is underway.Disclosure of InterestNone declared
Natural selection on gene expression Gilad, Yoav; Oshlack, Alicia; Rifkin, Scott A.
Trends in genetics,
08/2006, Letnik:
22, Številka:
8
Journal Article
Recenzirano
Changes in genetic regulation contribute to adaptations in natural populations and influence susceptibility to human diseases. Despite their potential phenotypic importance, the selective pressures ...acting on regulatory processes in general and gene expression levels in particular are largely unknown. Studies in model organisms suggest that the expression levels of most genes evolve under stabilizing selection, although a few are consistent with adaptive evolution. However, it has been proposed that gene expression levels in primates evolve largely in the absence of selective constraints. In this article, we discuss the microarray-based observations that led to these disparate interpretations. We conclude that in both primates and model organisms, stabilizing selection is likely to be the dominant mode of gene expression evolution. An important implication is that mutations affecting gene expression will often be deleterious and might underlie many human diseases.
Although it has been hypothesized for thirty years that many human adaptations are likely to be due to changes in gene regulation, almost nothing is known about the modes of natural selection acting ...on regulation in primates. Here we identify a set of genes for which expression is evolving under natural selection. We use a new multi-species complementary DNA array to compare steady-state messenger RNA levels in liver tissues within and between humans, chimpanzees, orangutans and rhesus macaques. Using estimates from a linear mixed model, we identify a set of genes for which expression levels have remained constant across the entire phylogeny (∼70 million years), and are therefore likely to be under stabilizing selection. Among the top candidates are five genes with expression levels that have previously been shown to be altered in liver carcinoma. We also find a number of genes with similar expression levels among non-human primates but significantly elevated or reduced expression in the human lineage, features that point to the action of directional selection. Among the gene set with a human-specific increase in expression, there is an excess of transcription factors; the same is not true for genes with increased expression in chimpanzee.
Currently there is no method of best practice for the normalization of microRNA sequencing data (miRNA-Seq). Therefore, we read with interest a recent article in RNA by Garmire and Subramaniam that ...set out to compare various normalization strategies specifically for this application (Garmire and Subramaniam 2012). They compared methods currently in use for normalization of messenger RNA sequencing (mRNA-Seq) data, such as total-depth normalization ("raw") and Trimmed Mean of M-values ("TMM"). Additionally, they compared many methods not used previously with sequencing data, such as global scaling, and borrowed from strategies applied to microarray studies, such as quantile normalization (QN). The article attracted our attention for many reasons, but notably for the claimed poor performance and "abnormal results" of our TMM method (Robinson and Oshlack 2010). After investigating, we discovered that TMM's claimed poor performance was the result of an error that shifted log-ratios in the wrong direction. Furthermore, we felt that various practical issues were not satisfyingly discussed; we comment briefly on these here and provide reproducible re-analyses to support our claims (see Supplemental Material).
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