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To determine whether sialyltransferases, sulfotransferases, and/or MUC genes are expressed and if they are induced by PMA

ABSTRACT: We are interested in having the gene microarray done on untreated and PMA treated (10 nM x 24 hr) human and mouse epithelial cells lines including CALU-3, MLE-15, primary bronchial human airway epithelial cells. We are especially interested in seeing whether sialyl or sulfo transferases, and MUC genes, are present and if they are induced by PMA. We hope to use this information to optimize future experiments designed to identify Siglec lung ligands. The lab is interested in studying untreated and PMA treated (10 nM x 24 hr) human and mouse epithelial cells lines including CALU-3, MLE-15, primary bronchial human airway epithelial cells. With special interest in understanding whether sialyl or sulfo transferases, and MUC genes, are present and if they are induced by PMA.

ORGANISM(S): Mus musculus

SUBMITTER: Steven Head

PROVIDER: E-GEOD-31992 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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To determine whether sialyltransferases, sulfotransferases, and/or MUC genes are expressed and if they are induced by PMA

Project description:We are interested in having the gene microarray done on untreated and PMA treated (10 nM x 24 hr) human and mouse epithelial cells lines including CALU-3, MLE-15, primary bronchial human airway epithelial cells. We are especially interested in seeing whether sialyl or sulfo transferases, and MUC genes, are present and if they are induced by PMA. We hope to use this information to optimize future experiments designed to identify Siglec lung ligands.

2011-09-08 | GSE31992 | GEO

Analysis of the apical secretome of Calu-3 and NHBE cells in 3D models of the human bronchial epithelium

Project description:The mucus secreted by airway epithelial cells plays a key role in the protection against and clearance of particles and pathogens. In this project, a 3D model of the bronchial epithelium was established using Calu-3 cells grown on porous inserts at the air-liquid interface. The secreted proteins were characterized in long-term cultures and compared to the apical secretome of primary normal human bronchial epithelial (NHBE) cells. The apical secretome was collected and characterized in the Calu-3 model at day 4, day 11, and day 18 after air-liquid interface and in the NHBE model at day 4, day 12, and day 18 after air-liquid interface. "This project received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement no 760928 (BIORIMA)."

2021-03-26 | PXD024242 | Pride

Changes in microRNA and mRNA expression with differentiation of human bronchial epithelial cells [mRNA]

Project description:Normal human bronchial epithelial (NHBE) cells cultured in an air-liquid interface (ALI) system form a polarized, pseudostratified epithelium composed of basal, ciliated and goblet cells that closely resemble the in vivo airway epithelium structure. ALI cultures of NHBE cells provide a unique in vitro system to investigate airway epithelial biology, including developmental, structural and physiologic aspects. In this study, we wanted to investigate mRNA expression patterns during airway epithelium differentiation. By using microarrays, we studied the changes in expression of mRNAs in normal human bronchial epithelial cells as they differentiate from an undifferentiated monolayer to a differentiated pseudostratified epithelium after 28 days of air-liquid interface (ALI) culture, when epithelial cells differentially express basal, ciliated and goblet cell markers. Normal human bronchial epithelial cells were cultured in an air-liquid interface (ALI) system and harvested at three different time-points: subconfluent, confluent and day 28 of ALI. Samples were processed for total RNA extraction and hybridization on Affymetrix microarrays. All the experiments were performed by triplicate.

2012-10-01 | E-GEOD-39059 | biostudies-arrayexpress

SARS-CoV-2 infection evokes transcriptional changes in Calu-3 cells and cultured primary mouse trigeminal ganglia cells

Project description:SARS-CoV-2, the virus responsible for COVID-19, infects both human airway epithelial cells and trigeminal ganglia. We assessed the consequences of SARS-CoV-2 infection on gene expression in Calu-3 cells and in primary Mus musculus trigeminal ganglia cells (mmTG). Here, we provide datasets that include raw reads and mapped reads for the following: 1) mock infected mmTG 48 hrs post infection; 2) SARS-CoV-2 infected mmTG 48 hrs post infection; 3) mock infected Calu-3 cells 24 hrs post infection; 4) SARS-CoV-2 infected Calu-3 cells 24 hrs post infection; 5) mock infected Calu-3 cells 48 hrs post infection; 6) SARS-CoV-2 infected Calu-3 cells 48 hrs post infection.

2024-01-08 | GSE252056 | GEO

Genome-wide distribution analysis of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early male embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT) and in absence of CLAMP

Project description:Purpose: Study how maternal Pioneer Transcription factor CLAMP affects sex-specifc splicing during initial embryonic development by regulating occupancy of spliceosome component Maleless (MLE), a RNA helicase on chromatin Method: Cut and Run (CUT&RUN) DNA libraries (Uyehara and McKay 2019) using anti-MLE antibody were generated from male embryos at 0-2 Hr pre-MZT and 2-4 hr post-MZT stages in presence and absence of maternal CLAMP. Maternal CLAMP was depleted by driving UAS-CLAMPRNAi in the ovaries using MTD-GAL4 maternal triple driver. As a control UAS-GFPRNAI was driven using the MTD-GAL4. Embryos were sexed using the meiotic drive system that produces sperm with only Y chromosomes (Reider et al 2017), resulting in progeny of only male genotypes. Results: We identified regions on chromatin where MLE binds during 0-2 Hr pre-MZTand 2-4 Hr post-MZT embryonic stages in males. In 0-2 Hr and 2-4 Hr old control embryos 28,279 and 24,910 MLE peaks were detected. After depletion of maternal CLAMP, 41.97% of 0-2 Hr peaks (22183 remaining, 6096 lost) and 59.1% of 2-4 Hr peaks (15735 remaining, 9175 lost) are lost. We also found loss of maternal CLAMP resulted in 26% and 35.25% new MLE peaks at 0-2 hr pre-MZT and 2-4 Hr post-MZT embryonic stages. Our motif search shows presence of putative motifs for MLE binding on chromatin which needs further validation. Conclusion: This is the first study showing genome-wide MLE occupancy in sexed embryos during 0-2 hr pre-MZT and 2-4 hr post-MZT stages. We show that the maternally deposited transcription factor CLAMP affects MLE occupancy on chromatin in early embryos. Thus, we conclude that maternal transcription factors can affect spliceosome function by regulating occupancy of their components on chromatin.

2022-05-01 | GSE174781 | GEO

Genome-wide analysis of distribution of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early female embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT)

Project description:Transcription factor CLAMP associates with RNA helicase, Maleless MLE as part of Male-specific MSL complex in males, which regulates dosage compensation in males. Both CLAMP and MLE are maternally deposited proteins (protein expression detectd in 0- Hr embryo, before zygotic genome activation) and MLE is also a conserved component of spliceosome. Moreover, CLAMP too associates with many other RNA binding protein compoments of spliceosomes. Both these proteins are well expressed in females, but apart from that might influence splicing in females, not much is known if they have any female-specific function. Furthermore, whether they regulate each other's function in females is not known as well, especially before zygotic genome activation starts, in a pre-MZT embryo (0-2 Hr Embryo). Therefore, we performed CutnRun assay to detrmine MLE binding sites on chromatin in female embryos before (0-2 Hr) and after MZT (2-4 Hr). And then identify, in absence of maternal CLAMP, whether there is change is distribution of control MLE female peaks. We identified regions on chromatin where MLE binds during 0-2 Hr pre-MZT and 2-4 Hr post-MZT embryonic stages in females. CLAMP unlike to males do not affect MLE distribution on chromatin in females.

2023-12-31 | GSE220981 | GEO

Changes in microRNA and mRNA expression with differentiation of human bronchial epithelial cells [mRNA]

2012-10-01 | GSE39059 | GEO

Molecular characterization of gene regulatory networks in primary human tracheal and bronchial epithelial cells.

Project description:The epithelial layer lining the airways has a central role in maintaining lung health, particularly serving as a barrier to prevent infection and delivery of harmful particles, which are cleared from the lung on the mucociliary escalator driven by the epithelium. Robust methods to culture primary airway epithelial cells were developed several decades ago and these cells provide the model of choice to investigate many diseases of the human lung. However, to date the molecular signature of cells from different regions of the airway epithelium has not been well characterized. Here we examine primary cells derived from human tracheal and bronchial tissues and perform genome-wide analysis of their active regulatory elements and gene expression profiles. We also compare cells from healthy and diseased (cystic fibrosis) donor lung tissue. Our data reveal an airway cell signature that is divergent from other epithelial cell types and from immortalized or transformed airway epithelial cell lines. The differences between tracheal and bronchial cells are clearly evident as are common regulatory features between the cell types of two different origins. Only minor variation is seen between cells from healthy or CF bronchial cells. These data are a valuable resource for functional genomics analysis of airway epithelial tissues in human health and disease.

2018-02-28 | GSE101993 | GEO

IL-13 stimulation of primary human bronchial epithelial cells in control individuals and patients with asthma.

Project description:We performed RNA sequencing of gene expression of differentiated primary human bronchial epithelial cells derived from control and asthmatic patients, stimulated with IL-13. The Type 2 Asthma mediator IL-13 was described to induce airway hyperresponsiveness, goblet cell metaplasia, mucus hypersecretion and airway remoddeling including impairment of epithelial barrier integrity. We investigated differential expression of SARS-CoV-2 related host gene expression as well as genes involved in N-linked glycosylation upon IL-13 in bronchial epithelial cells. Top IL-13 affected pathways included ion- and transmembrane transport, lipid metabolic processed and protein glycosylation.

2023-01-30 | GSE206510 | GEO

BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (IV)

Project description:Background: We got interested whether genes of airway basal cells are enriched in COPD. Methods: Bronchoscopy with bronchial brushes and bronchoalveolar lavage was performed in 28 patients with COPD and 29 healthy donors and isolated BAL cells.Transcriptome of BAL cells were studied by using Affymetrix Human Genome U133 Plus 2.0 array on an Affymetrix platform. Microarray data were normalized data were imported, log2-transformed and quantile normalized using robust multi-array average (RMA). We tested enrichment for airway basal cells by ROMER enrichment analysis. Results: we did not find enrichment of airway basal cell genes in COPD compared to healthy volunteers.

2018-12-31 | GSE73395 | GEO

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