2,110 research outputs found
Molecular signatures distinguish human central memory from effector memory CD8 T cell subsets
Abstract
Memory T cells are heterogeneous in terms of their phenotype and functional properties. We investigated the molecular profiles of human CD8 naive central memory (TCM), effector memory (TEM), and effector memory RA (TEMRA) T cells using gene expression microarrays and phospho-protein-specific intracellular flow cytometry. We demonstrate that TCM have a gene expression and cytokine signaling signature that lies between that of naive and TEM or TEMRA cells, whereas TEM and TEMRA are closely related. Our data define the molecular basis for the different functional properties of central and effector memory subsets. We show that TEM and TEMRA cells strongly express genes with known importance in CD8 T cell effector function. In contrast, TCM are characterized by high basal and cytokine-induced STAT5 phosphorylation, reflecting their capacity for self-renewal. Altogether, our results distinguish TCM and TEM/TEMRA at the molecular level and are consistent with the concept that TCM represent memory stem cells.</jats:p
Human naive CD8 T cells down-regulate expression of the WNT pathway transcription factors lymphoid enhancer binding factor 1 and transcription factor 7 (T cell factor-1) following antigen encounter in vitro and in vivo
Abstract
The transcription factors lymphoid enhancer binding factor 1 (LEF1) and transcription factor 7 (TCF7) (T cell factor-1 (TCF-1)) are downstream effectors of the WNT signaling pathway, which is a critical regulator of T cell development in the thymus. In this study, we show that LEF1 and TCF7 (TCF-1) are not only expressed in thymocytes, but also in mature T cells. Our data demonstrate that Ag encounter in vivo and engagement of the TCR or IL-15 receptor in vitro leads to the down-regulation of LEF1 and TCF7 (TCF-1) expression in human naive CD8 T cells. We further show that resting T cells preferentially express inhibitory LEF1 and TCF7 (TCF-1) isoforms and that T cell activation changes the isoform balance in favor of stimulatory TCF7 (TCF-1) isoforms. Altogether, our study suggests that proteins involved in the WNT signaling pathway not only regulate T cell development, but also peripheral T cell differentiation.</jats:p
Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis
BACKGROUND: Cell-based microarrays were first described by Ziauddin and Sabatini in 2001 as a powerful new approach for performing high throughput screens of gene function. An important application of cell-based microarrays is in screening for proteins that modulate gene networks. To this end, cells are grown over the surface of arrays of RNAi or expression reagents. Cells growing in the immediate vicinity of the arrayed reagents are transfected and the arrays can then be scanned for cells showing localised changes in function. Here we describe the construction of a large-scale microarray using expression plasmids containing human genes, its use in screening for genes that induce apoptosis when over-expressed and the characterisation of a number of these genes by following the transcriptional response of cell cultures during their induction of apoptosis. RESULTS: High-density cell-based arrays were successfully fabricated using 1,959 un-tagged open reading frames (ORFs) taken from the Mammalian Gene Collection (MGC) in mammalian expression vectors. The arrays were then used to screen for genes inducing apoptosis in Human Embryonic Kidney (HEK293T) cells. Using this approach, 10 genes were clearly identified and confirmed to induce apoptosis. Some of these genes have previously been linked to apoptosis, others not. The mechanism of action of three of the 10 genes were then characterised further by following the transcriptional events associated with apoptosis induction using expression profiling microarrays. This data demonstrates a clear pro-apoptotic transcriptional response in cells undergoing apoptosis and also suggests the use of common apoptotic pathways regardless of the nature of the over-expressed protein triggering cell death. CONCLUSION: This study reports the design and use of the first truly large-scale cell-based microarrays for over-expression studies. Ten genes were confirmed to induce apoptosis, some of which were not previously known to possess this activity. Transcriptome analysis on three of the 10 genes demonstrated their use of similar pathways to invoke apoptosis
Visualisation of BioPAX Networks using BioLayout Express (3D).
BioLayout Express (3D) is a network analysis tool designed for the visualisation and analysis of graphs derived from biological data. It has proved to be powerful in the analysis of gene expression data, biological pathways and in a range of other applications. In version 3.2 of the tool we have introduced the ability to import, merge and display pathways and protein interaction networks available in the BioPAX Level 3 standard exchange format. A graphical interface allows users to search for pathways or interaction data stored in the Pathway Commons database. Queries using either gene/protein or pathway names are made via the cPath2 client and users can also define the source and/or species of information that they wish to examine. Data matching a query are listed and individual records may be viewed in isolation or merged using an 'Advanced' query tab. A visualisation scheme has been defined by mapping BioPAX entity types to a range of glyphs. Graphs of these data can be viewed and explored within BioLayout as 2D or 3D graph layouts, where they can be edited and/or exported for visualisation and editing within other tools
Perceived speed at low luminance: Lights out for the Bayesian observer?
To account for perceptual bias, Bayesian models use the precision of early sensory measurements to weight the influence of prior expectations. As precision decreases, prior expectations start to dominate. Important examples come from motion perception, where the slow-motion prior has been used to explain a variety of motion illusions in vision, hearing, and touch, many of which correlate appropriately with threshold measures of underlying precision. However, the Bayesian account seems defeated by the finding that moving objects appear faster in the dark, because most motion thresholds are worse at low luminance. Here we show this is not the case for speed discrimination. Our results show that performance improves at low light levels by virtue of a perceived contrast cue that is more salient in the dark. With this cue removed, discrimination becomes independent of luminance. However, we found perceived speed still increased in the dark for the same observers, and by the same amount. A possible interpretation is that motion processing is therefore not Bayesian, because our findings challenge a key assumption these models make, namely that the accuracy of early sensory measurements is independent of basic stimulus properties like luminance. However, a final experiment restored Bayesian behaviour by adding external noise, making discrimination worse and slowing perceived speed down. Our findings therefore suggest that motion is processed in a Bayesian fashion but based on noisy sensory measurements that also vary in accuracy
From filters to features:Scale-space analysis of edge and blur coding in human vision
To make vision possible, the visual nervous system must represent the most informative features in the light pattern captured by the eye. Here we use Gaussian scale-space theory to derive a multiscale model for edge analysis and we test it in perceptual experiments. At all scales there are two stages of spatial filtering. An odd-symmetric, Gaussian first derivative filter provides the input to a Gaussian second derivative filter. Crucially, the output at each stage is half-wave rectified before feeding forward to the next. This creates nonlinear channels selectively responsive to one edge polarity while suppressing spurious or "phantom" edges. The two stages have properties analogous to simple and complex cells in the visual cortex. Edges are found as peaks in a scale-space response map that is the output of the second stage. The position and scale of the peak response identify the location and blur of the edge. The model predicts remarkably accurately our results on human perception of edge location and blur for a wide range of luminance profiles, including the surprising finding that blurred edges look sharper when their length is made shorter. The model enhances our understanding of early vision by integrating computational, physiological, and psychophysical approaches. © ARVO
Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment
Background: Biopsies taken from individual tumours exhibit extensive differences in their cellular composition due to the inherent heterogeneity of cancers and vagaries of sample collection. As a result genes expressed in specific cell types, or associated with certain biological processes are detected at widely variable levels across samples in transcriptomic analyses. This heterogeneity also means that the level of expression of genes expressed specifically in a given cell type or process, will vary in line with the number of those cells within samples or activity of the pathway, and will therefore be correlated in their expression.Results: Using a novel 3D network-based approach we have analysed six large human cancer microarray datasets derived from more than 1,000 individuals. Based upon this analysis, and without needing to isolate the individual cells, we have defined a broad spectrum of cell-type and pathway-specific gene signatures present in cancer expression data which were also found to be largely conserved in a number of independent datasets.Conclusions: The conserved signature of the tumour-associated macrophage is shown to be largely-independent of tumour cell type. All stromal cell signatures have some degree of correlation with each other, since they must all be inversely correlated with the tumour component. However, viewed in the context of established tumours, the interactions between stromal components appear to be multifactorial given the level of one component e.g. vasculature, does not correlate tightly with another, such as the macrophage
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Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins.
BACKGROUND: The combination of complete genome sequence information with expression data enables us to characterize the relationship between a protein's evolutionary origin or functional category and its expression pattern. In this study, mouse proteins were assigned into functional and phyletic groups and the gene expression patterns of the different protein groupings were examined by microarray analysis in various mouse tissues. RESULTS: Our results suggest that the proteins that are universally distributed in all tissues are predominantly enzymes and transporters. In contrast, the tissue-specific set is dominated by regulatory proteins (signal transduction and transcription factors). An increased tendency to tissue-specificity is observed for metazoan-specific proteins. As the composition of the phyletic groups highly correlates with that of the functional groups, the data were tested in order to determine which of the two factors -- function or phyletic age -- is dominant in shaping the expression profile of a protein. The observed differences in expression patterns of genes between functional groups were found mainly to reflect their different phyletic origin. The connection between tissue specificity and phyletic age cannot be explained by the recent rate of evolution. Finally, although metazoan-specific proteins tend to be tissue-specific compared with phyletically conserved proteins present in all domains of life, many such 'universal' proteins are also tissue-specific. CONCLUSION: The minimal cellular transcriptome of the metazoan cell differs from that of the ancestral unicellular eukaryote: new functions were added (metazoan-specific proteins), whilst other functions became specialized and no longer took place in all cells (tissue-specific pre-metazoan proteins).RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are
Saccadic compensation for reflexive optokinetic nystagmus just as good as compensation for volitional pursuit
The natural viewing behavior of moving observers ideally requires target-selecting saccades to be coordinated with automatic gaze-stabilizing eye movements such as optokinetic nystagmus. However, it is unknown whether saccade plans can compensate for reflexive movement of the eye during the variable saccade latency period, and it is unclear whether reflexive nystagmus is even accompanied by extraretinal signals carrying the eye movement information that could potentially underpin such compensation. We show that saccades do partially compensate for optokinetic nystagmus that displaces the eye during the saccade latency period. Moreover, this compensation is as good as for displacements due to voluntary smooth pursuit. In other words, the saccade system appears to be as well coordinated with reflexive nystagmus as it is with volitional pursuit, which in turn implies that extraretinal signals accompany nystagmus and are just as informative as those accompanying pursuit
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