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Contrasting gene expression patterns associated with high and low rhinovirus stimulated IFN-α production

ABSTRACT: Contrasting gene expression patterns associated with high and low rhinovirus stimulated IFN-α production

PROVIDER: PRJNA700069 | ENA |

REPOSITORIES: ENA

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Contrasting gene expression patterns associated with high and low rhinovirus stimulated IFN-α production

Project description:Introduction: Viral respiratory infections cause considerable morbidity and economic loss. While rhinoviruses (RV) typically cause little more than the common cold, they can produce severe infections and disease exacerbations in susceptible individuals, including those with chronic lung diseases. Variations in the regulation of key antiviral cytokines, particularly type I interferon (IFN-α and IFN-b), may contribute to RV susceptibility, but are not well understood. Method: Whole genome transcription patterns were assessed in samples from 74 individuals demonstrating high or low IFN-α production following RV stimulation in vitro. Results: In unstimulated samples (baseline) the high IFN-α producer group showed higher expression of genes associated with plasmacytoid dendritic cells, the complement system, B-cell chemokines, immune regulation, macrophages, and vitamin D activation and lower expression of genes linked to haemoglobin and haem biosynthesis, wound healing, stress response and pro-inflammatory genes than the low IFN-α producer group. After RV stimulation, the high IFN-α producer group showed more intense upregulation of diverse immune function genes including IFNs and greater downregulation of genes linked to structural and extra-cellular matrix functions than the low IFN-α producer group. Patterns of antibacterial gene expression varied between groups. Healthy people and those with asthma generally showed similar gene expression patterns. These findings highlight multiple biological pathways whose expression patterns differ substantially between high and low IFN-α producers. These differences likely contribute to variations in anti-RV immunity and immunopathology between individuals.

2021-07-31 | GSE166292 | GEO

Rhinovirus stimulated IFN-? production: how important are plasmacytoid DCs, monocytes and endosomal pH?

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Rhinovirus C

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Contrasting patterns of microbial dominance

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KBM7 genetrap mutant cells stimulated with TNF-alpha and IFN-gamma

Project description:Transcriptional response of KBM7 cells to IFN-gamma or TNF-alpha was investigated in control or cells with genetrap insertions in JAK2 or TNFRS1A, respectively. The experiment shows that, as expected, cells lacking JAK2 or TNFRS1A expression display a severly blunted response to the tested cytokines. KBM7 genetrap mutant cells stimulated with TNF-alpha and IFN-gamma Sample WT_1 corresponds with the control sample for the IFN-gamma stimulation; Sample WT_2 corresponds with the control sample for the TNF-alpha stimulation. As the expected differences between the samples was large, only single replicates were performed for each condition

2013-08-09 | E-GEOD-48848 | biostudies-arrayexpress

Rhinovirus C

Project description:Human rhinovirus C overview

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IFN-alpha Stimulated Gene Expression in Sensitive and Resistant Renal Cell Carcinoma Cell Lines

Project description:The antiproliferative, antiviral, and immunomodulatory properties of interferons (IFNs) have led to its therapeutic implementation. IFNs effects are mediated by a complex network of signal transducers, culminating in IFN-stimulated gene (ISG) induction. This complexity leads to diverse clinical responses to IFN, from no response to complete regression of disease. Elucidation of ISG induction patterns is, therefore, essential to understand and maximize its therapeutic potential. To correlate ISG expression profiles with IFN responsiveness, two renal cell carcinoma (RCC) cell lines differing in antiviral and apoptotic response to IFN were treated with IFN-alpha for different times, and expression profiles were analyzed using a customized microarray containing 850 unique putative ISGs. Genes with similar kinetics of induction in both cell lines were clustered and analyzed for gene function. Seven sets of coordinately regulated genes were identified by k-means cluster analysis, and significant functional similarities were identified for five of the seven sets. Strikingly, expression of genes associated with transcription temporally preceded expression of those involved in signal transduction. Enhanced antiviral sensitivity to IFN was coincident with sustained expression of ISGs involved in transcriptional regulation. However, no difference in Stat1 activation was observed between the cell lines. Analysis of ISG expression patterns suggests that subtle differences in transcription profiles contribute to differences in IFN responsiveness. Two human renal cell carcinoma cell lines (ACHN and RCC1) were treated with IFN-alpha for 3, 6, 9, 12, 16, and 24 hours. Total RNA from treated cells (Cy5) is hybridized with total RNA from untreated control cells (Cy3) to the custom ISG 1.3.1 cDNA array.

2010-05-18 | E-GEOD-15193 | biostudies-arrayexpress

Gene expression in human macrophages stimulated with IFN-alpha and IL10

Project description:Human monocyte-derived macrophages were stimulated with IFN-alpha or IL-10, and then gene expression was evaluated.

2021-03-01 | GSE114841 | GEO

Global transcriptional changes induced by rhinovirus infection in-vitro

Project description:Cell lines B2B and 16HBE were infected in-vitro with rhinovirus 16 and comparisons were made to mock-infected cultures and cultures exposed to UV-irradiated rhinovirus. Total RNA were extracted and assessed by whole genome expression arrays. Rhinovirus in-vitro infected cell lines harvested at different time points (T hours) in biological triplicates. Total RNA extracted directly upon harvest.

2014-04-01 | E-GEOD-28904 | biostudies-arrayexpress

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