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Expression data from unactivated vs. activated PBMCs (ion array)

ABSTRACT: Long-lasting activation of T cells requires up-regulation of many genes, for example of transcription factors, cytoskeletal proteins and cell surface proteins encluding ion channels. An increase of ion channel density at the cell surface reflects the needs to manage increased Ca2+ influx into the activated T cell. Using oligonucleotide-based arrays we have surveyed changes in ion channel mRNA expression that occur upon T cell activation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE22387 | GEO | 2010/06/17

SECONDARY ACCESSION(S): PRJNA127739

REPOSITORIES: GEO

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Expression data from unactivated vs. activated PBMCs (ion array)

Project description:Long-lasting activation of T cells requires up-regulation of many genes, for example of transcription factors, cytoskeletal proteins and cell surface proteins encluding ion channels. An increase of ion channel density at the cell surface reflects the needs to manage increased Ca2+ influx into the activated T cell. Using oligonucleotide-based arrays we have surveyed changes in ion channel mRNA expression that occur upon T cell activation. We isolated PBMCs from blood of healthy donors and divided those into two parts. One was activated for 72 hr by adding PHA-L whereas the other part was incubated in the same way but not stimulated.

2010-06-17 | E-GEOD-22387 | biostudies-arrayexpress

Expression data from unactivated vs. activated PBMCs

Project description:Long-lasting activation of T cells requires up-regulation of many genes, for example of transcription factors, cytoskeletal proteins and cell surface proteins encluding ion channels. An increase of ion channel density at the cell surface reflects the needs to manage increased Ca2+ influx into the activated T cell. Using oligonucleotide-based arrays we have surveyed changes in ion channel mRNA expression that occur upon T cell activation. We used Affymetrix Analysis to confirmate our data achieved by self-designed glass array analysis.

2010-05-14 | GSE21837 | GEO

Expression data from unactivated vs. activated PBMCs

Project description:Long-lasting activation of T cells requires up-regulation of many genes, for example of transcription factors, cytoskeletal proteins and cell surface proteins including ion channels. An increase of ion channel density at the cell surface reflects the needs to manage increased Ca2+ influx into the activated T cell. Using oligonucleotide-based arrays we have surveyed changes in ion channel mRNA expression that occur upon T cell activation. We used Affymetrix Analysis to confirm our data achieved by self-designed glass array analysis. We isolated PBMCs from blood of healthy donors and divided those into two parts. One was activated for 72 hr by adding PHA-L whereas the other part was incubated in the same way but not stimulated.

2010-05-28 | E-GEOD-21837 | biostudies-arrayexpress

Wnt signaling regulates ion channel expression to promote smooth muscle and cartilage formation in developing mouse trachea

Project description:Ion channels play critical roles in the physiology and function of the nervous system and contractile tissue; however, their role in non-contractile tissue and embryonic development has yet to be understood. Tracheobronchomalacia (TBM) and complete tracheal rings (CTR) are disorders affecting the muscle and cartilage of the trachea and bronchi, whose etiology remains poorly understood. We demonstrated that trachealis muscle organization and polarity are disrupted after epithelial ablation of Wls, a cargo receptor critical for the Wnt signaling pathway, in developing trachea. The phenotype resembles the anomalous trachealis muscle observed after deletion of ion channel encoding genes in developing mouse trachea. We sought to investigate whether and how the deletion ofWlsaffects ion channels during tracheal development. We hypothesize that Wnt signaling influences the expression of ion channels to promote trachealis muscle cell assembly and patterning. Deleting Wls in developing trachea causes differential regulation of genes mediating actin binding, cytoskeleton organization, and potassium ion channel activity. Wnt signaling regulated expression of Kcnj13, Kcnd3, Kcnj8, and Abcc9 as demonstrated by in vitro studies and in vivo analysis in Wnt5a and b-catenin deficient tracheas. Pharmacological inhibition of potassium ion channels and Wnt signaling impaired contractility of developing trachealis smooth muscle and formation of cartilaginous mesenchymal condensation. Thus, in mice, epithelial-induced Wnt/b-catenin signaling mediates trachealis muscle and cartilage development via modulation of ion channel expression, promoting trachealis muscle architecture, contractility, and cartilaginous extracellular matrix. In turn, ion channel activity may influence tracheal morphogenesis underlying TBM and CTR.

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Transcription Factor Acj6 Controls Dendrite Targeting via Combinatorial Cell-Surface Codes

Project description:Transcription factors specify the fate and connectivity of developing neurons. We investigate how a lineage-specific transcription factor, Acj6, controls the precise dendrite targeting of Drosophila olfactory projection neurons (PNs) by regulating the expression of cell-surface proteins. Quantitative cell-surface proteomic profiling of wild-type and acj6 mutant PNs in intact developing brains and a proteome-informed genetic screen identified PN surface proteins that execute Acj6-regulated wiring decisions. These include canonical cell adhesion molecules and proteins previously not associated with wiring, such as Piezo, whose mechanosensitive ion channel activity is dispensable for its function in PN dendrite targeting. Comprehensive genetic analyses revealed that Acj6 employs unique sets of cell-surface proteins in different PN types for dendrite targeting. Combinatorial expression of Acj6 wiring executors rescued acj6 mutant phenotypes with higher efficacy and breadth than expression of individual executors. Thus, Acj6 controls wiring specificity of different neuron types by specifying distinct combinatorial expression of cell-surface executors.

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Nitrogen-ion-beam implantation effect on rice dry seeds

Project description:Analysis of 96-hours-old-rice seedlings with promoted-growth induced by implantation with low-energy nitrogen ion beam. Ion-beam implantation can induce changes in 351 up-regulated transcripts and 470 down-regulated transcripts, including signaling proteins, kinases, plant hormones, transposable elements, transcription factors, non-coding protein RNAs, secondary metabolites, resistance proteins, peroxidase, chromatin modification and even miRNAs. Results provide insight into the molecular basis of biological effects of plants that implanted by ion beam.

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Identification of cardiac ion channel protein networks and their signature in the human electrocardiogram

Project description:Protein-protein interactions are essential for normal cellular processes and signaling events. Defining these interaction networks is therefore crucial for understanding complex cellular functions and interpretation of disease-associated gene variants. We need to build a comprehensive picture of the interactions, their affinities and interdependencies in the specific organ and cell-type to understand hitherto poorly understood signaling mechanism through ion channels and to begin their mechanistic studies. Here, we experimentally identify the ensemble of interacting partners for 13 types of ion channel in murine cardiac tissue to understand their role in cardiomyocyte electrophysiology. Of these, we validated the functional importance of 10 novel interactors on cardiac electrophysiology through genetic knockouts in zebrafish, super resolution microscopy, and patch clamp experiments. Furthermore, we establish a computational framework to reconstruct human cardiomyocyte ion channel networks from deep proteome mapping of human heart tissue and human heart single-cell gene-expression data. Finally, we integrate the ion channel interactome with human population genetics data to identify proteins that influence the electrocardiogram (ECG). The combined channel network is enriched for proteins influencing the ECG; with 44% of the network proteins significantly associated with an ECG phenotype. Altogether, we comprehensively define the interactomes of 13 major cardiac ion channels, contextualize their relevance to human electrophysiology including impact on the ECG, and validate the functional roles of ten novel interactors, thereby creating a roadmap for our understanding of how ion channel interactomes regulate cardiac electrophysiology.

2023-09-18 | PXD028021 | Pride

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