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Early Detection of Peripheral Blood Cell Signature in Children Developing Beta-Cell Autoimmunity at a Young Age
<p>The appearance of Type 1 diabetes (T1D)-associated autoantibodies is the
first and only measurable parameter to predict progression toward T1D
in genetically susceptible individuals. However, autoantibodies indicate
...
snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions
<h4>Motivation: </h4><p>Co-localization of trait associated SNPs for
specific transcription-factor binding sites or regulatory regions in the
genome can yield profound insight into underlying causal mechanisms.
Analysis ...
DNA methylation and Transcriptome Changes Associated with Cisplatin Resistance in Ovarian Cancer
<p>
</p><p>High-grade serous
ovarian cancer is the most common ovarian cancer type. Although the combination
of surgery and platinum-taxane chemotherapy provide an effective treatment,
drug resistance frequently ...
Serum Proteomic Profiling to Identify Biomarkers of Premature Carotid Atherosclerosis
<p>To evaluate the presence of serum protein biomarkers associated with the early phases of formation of carotid atherosclerotic plaques, label-free quantitative proteomics analyses were made for serum samples collected ...
Quantitative genome-scale metabolic modeling of human CD4+ T cell differentiation reveals subset-specific regulation of glycosphingolipid pathways
<p>T cell activation, proliferation, and differentiation involve metabolic reprogramming resulting from the interplay of genes, <a href="https://www.sciencedirect.com/topics/neuroscience/proteome" title="Learn more about proteins from ScienceDirect's AI-generated Topic Pages">proteins</a>, and metabolites. Here, we aim to understand the <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/metabolic-pathways" title="Learn more about metabolic pathways from ScienceDirect's AI-generated Topic Pages">metabolic pathways</a> involved in the activation and functional differentiation of human CD4<sup>+</sup> T cell subsets (T helper [Th]1, Th2, Th17, and induced regulatory T [iTreg] cells). Here, we combine genome-scale metabolic modeling, gene expression data, and targeted and non-targeted <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/lipidomics" title="Learn more about lipidomics from ScienceDirect's AI-generated Topic Pages">lipidomics</a> experiments, together with in vitro <a href="https://www.sciencedirect.com/topics/immunology-and-microbiology/gene-knockdown" title="Learn more about gene knockdown from ScienceDirect's AI-generated Topic Pages">gene knockdown</a> experiments, and show that human CD4<sup>+</sup> T cells undergo specific metabolic changes during activation and functional differentiation. In addition, we confirm the importance of <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/ceramide" title="Learn more about ceramide from ScienceDirect's AI-generated Topic Pages">ceramide</a> and <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/glycosphingolipid" title="Learn more about glycosphingolipid from ScienceDirect's AI-generated Topic Pages">glycosphingolipid</a> <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/anabolism" title="Learn more about biosynthesis from ScienceDirect's AI-generated Topic Pages">biosynthesis</a> pathways in Th17 differentiation and effector functions. Through in vitro gene knockdown experiments, we substantiate the requirement of <a href="https://www.sciencedirect.com/topics/neuroscience/serine-palmitoyltransferase" title="Learn more about serine palmitoyltransferase from ScienceDirect's AI-generated Topic Pages">serine palmitoyltransferase</a> (SPT), a de novo <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/sphingolipid" title="Learn more about sphingolipid from ScienceDirect's AI-generated Topic Pages">sphingolipid</a> pathway in the expression of <a href="https://www.sciencedirect.com/topics/immunology-and-microbiology/proinflammatory-cytokine" title="Learn more about proinflammatory cytokines from ScienceDirect's AI-generated Topic Pages">proinflammatory cytokines</a> (interleukin [IL]-17A and IL17F) by <a href="https://www.sciencedirect.com/topics/immunology-and-microbiology/th17-cell" title="Learn more about Th17 cells from ScienceDirect's AI-generated Topic Pages">Th17 cells</a>. Our findings provide a comprehensive resource for selective manipulation of CD4<sup>+</sup> T cells under disease conditions characterized by an imbalance of Th17/natural Treg (nTreg) cells.</p>...
CIP2A Constrains Th17 Differentiation by Modulating STAT3 Signaling
Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) is an oncogene and a potential cancer therapy target protein. Accordingly, a better understanding of the physiological function of CIP2A, especially in the context of ...
RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells
<p>POLR3G is expressed at high levels in human pluripotent stem cells
(hPSCs) and is required for maintenance of stem cell state through
mechanisms not known in detail. To explore how POLR3G regulates stem
cell state, ...
An IFIH1 gene polymorphism associated with risk for autoimmunity regulates canonical antiviral defence pathways in Coxsackievirus infected human pancreatic islets
<p>The IFIH1 gene encodes the pattern recognition receptor MDA5. A common
polymorphism in IFIH1 (rs1990760, A946T) confers increased risk for
autoimmune disease, including type 1-diabetes (T1D). Coxsackievirus
infections ...
Analysis of the plasma proteome using iTRAQ and TMT-based Isobaric labeling
<p>Over the past decade, chemical labeling with isobaric tandem mass tags,
such as isobaric tags for relative and absolute quantification reagents
(iTRAQ) and tandem mass tag (TMT) reagents, has been employed in a wide ...
An additive Gaussian process regression model for interpretable non-parametric analysis of longitudinal data
<p>Biomedical research typically involves longitudinal study designs where
samples from individuals are measured repeatedly over time and the goal
is to identify risk factors (covariates) that are associated with an ...