Analysis of normal lung cells treated with 5-aza-dC to induce DNA demethylation
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE18454 | GEO | 2010/10/07
SECONDARY ACCESSION(S): PRJNA118169
REPOSITORIES: GEO
Similar Datasets
Project description:Analysis of 2 cultured normal lung cell lines, Normal Human Bronchial Epithelial (NHBE) and Human Small Airway Epithelial (SAEC) cells (Lonza, Walkersville, MD), following treatment with 5-aza-dC to induce DNA demethylation. These results provide insight into the role of epigenetic alterations, specifically demethylation, in differential gene expression in various lung neoplasms. Two normal lung cell lines, NHBE and SAEC, were treated with 5uM 5-aza deoxycytidine for 72 hours and Trichostatin A for 24 hours prior to harvesting total RNA for expression array analysis using the Affymetrix Human Genome U133 Plus 2.0 expression platform. Signal intensity and statistical significance was established for each transcript using dChip version 2005. Two-fold increase based on the 90% confidence interval of the result and expression minus baseline >50 was used as the statistical cutoff value after 5Aza-dC and/or TSA treatment to identify upregulated candidate genes.
2010-10-07 | E-GEOD-18454 | biostudies-arrayexpress
Project description:To investigate the biochemical and genetic alterations that occur in response to cigarette smoke exposure among airway epithelial cells from different sites in the lungs, we performed microarray-based analysis using small airway epithelial cells (SAEC) and normal human bronchial epithelial cells (NHBE) following 24 h of cigarette smoke extract (CSE). In microarray-based analysis, the small airway showed higher susceptibility to CS compared to the large airway, such as enhanced expression of inflammatory-related pathways including the TNF signaling pathway. Among the TNF-related genes, PTGS2, also known as COX-2, showed the greatest difference in expression levels, with higher CSE-induced increments of both mRNA and protein expression in SAEC compared to NHBE.
2018-01-16 | GSE107200 | GEO
Project description:To assess transcriptional regulation by DNA demethylation in SAEC, we carried out a microarray analysis of SAEC treated with a demethylating agent (5-aza-dC) and a HDAC inhibitor (TSA). We used the Agilent SurePrint G3 Human Gene Expression 8x60K v3 microarray which contains probes for 26,083 Entrez genes and 30,606 lncRNAs.
2017-06-28 | GSE82214 | GEO
Project description:The interaction of lung epithelial and lung mesenchymal cells (fibroblasts) was investigated in a novel co-culture model of human pulmonary fibrosis. Remarkably, co-culturing both cell types induced cell-type-specific responses, including fibroblast-to-myofibroblast differentiation and epithelial-to-mesenchymal transition (EMT), which were fully dependent on direct epithelial / fibroblast contact. Primary normal human lung fibroblasts (NHLF) and normal human bronchiolar epithelial cells (NHBE) were fluorescently labelled prior to seeding, then grown either as mono or co-cultures and collected in triplicates for mRNA-seq at the start (T=0h) and after 3h and 18h. Each harvested cell culture was FACS sorted into individual NHLF and NHBE cell populations, which were then then lysed and sequenced.
2022-10-03 | E-MTAB-11832 | biostudies-arrayexpress
Project description:The interaction of lung epithelial and lung mesenchymal cells was investigated in a novel co-culture model of human pulmonary fibrosis. Remarkably, co-culturing both cell types induced cell-type-specific responses, including fibroblast-to-myofibroblast differentiation and epithelial-to-mesenchymal transition (EMT), which were fully dependent on direct epithelial / fibroblast contact. We used single-cell RNA sequencing (scRNA-seq) to evaluate the transcriptional fate of the normal human lung fibroblasts (NHLF) and normal human bronchiolar epithelial cells (NHBE) during the course of co-cultivation, and compare the single cell profiles with their counterpart isolated from patients with idiopathic pulmonary fibrosis (IPF). NHLF and normal NHBE cells were grown as co-cultures, cell suspensions were collected at the time points t = 0h, 3h and 18h and analyzed by single-cell RNA-seq on a Chromium Platform. Eight samples were sequenced, resulting in a total of xx single cell transcription profiles.
2022-10-03 | E-MTAB-11847 | biostudies-arrayexpress
Project description:Measles virus infects serum activated airway epithelial cells and many adenocarcinoma cell lines. A microarray analysis was performed on virus permissive versus non-permissive cells. Membrane protein genes that were upregulated in permissive cells were tested as receptor/entry factors. Membrane protein genes that were upregulated in smooth airway epithelial cells (SAEC) following growth in 10% fetal calf serum that made the cell line permissive to measles virus were identified. Membrane protein genes that were upregulated in adenocarcinoma cells that were permissive to wild type measles virus infection were identified. [SAEC]: Airway cells (SAEC) grown in serum free media (SAGM) were purchaced from Lonza. Half the cells were cultured in SAGM, the other half were transferred into Dulbecco's 10% fetal calf serum for 24 hrs. RNA was harvested from the cells by the Qiagen RNAeasy [Adenocarcinoma cells]: MCF7, MDA-MB-468, T47D, NCI-H358, NCI-H125, MGH24 cells were permissive and A549 and MDA-MB-231 cells were non-permissive.
2011-07-28 | E-GEOD-26636 | biostudies-arrayexpress
Project description:Small cell lung cancer (SCLC) is a subtype of lung cancer with poor prognosis due to early dissemination and rapid growth. We here analyze gene expression profile of 23 clinical SCLC samples. EZH2 was found to be highly expressed in SCLC samples compared to 42 normal tissues including the normal lung, and other PRC2 members, SUZ12 and EED, were also highly expressed in SCLC. To obtain target genes of PRC2 in SCLC, H3K27me3 mark was mapped in three SCLC cell lines, Lu130, H209 and DMS53, and compared to normal small airway epithelial cells (SAEC). Whereas H3K27me3(+) genes in SAEC were significantly overlapped with PRC-target genes in ES cells (P=1.7x10-31), genes with H3K27me3 in SCLC cell lines but not in SAEC were not significantly overlapped with PRC-target genes in ES cells (P=0.64). These genes with H3K27me3 specifically in SCLC cell lines but not in SAEC showed decreased expression, not only in SCLC cell lines but also in clinical SCLCs, and showed enrichment of GO-terms such as plasma membrane (P=8.1x10-21) and cell adhesion (P=1.7x10-8). Introduction of JUB, a gene showing specific H3K27me3 modification and the strongest repression in the three SCLC cell lines, resulted in repression of cellular growth in DMS53. In clinical SCLC cases, lower JUB level correlated to shorter survival (P=0.002), or a set of PRC target genes (JUB, EPHB4) and marker genes of classic type SCLC (GRP, ASCL1) correlated to shorter survival (P=0.0001) and classified SCLC into two groups with distinct prognosis. Growth of SCLC cell lines was repressed when treated with 3-Deazaneplanocin A, an inhibitor against PRC2. It is suggested that high expression of PRC2 in SCLC contributed to repression of genes including non-PRC-target genes in ES cells, and that the gene repression may play a role in genesis of SCLC. Gene expression in 23 clinical SCLC samples, 42 normal tissue samples, 3 small cell lung cancer (SCLC) cell lines, and normal small airway epithelial cell (SAEC) was analyzed by Affymetrix arrays. This dataset is part of the TransQST collection.
2013-06-12 | E-GEOD-43346 | biostudies-arrayexpress
Project description:The goal of our study was to determine the effect the TRPV1 I585V SNP has on lung cells. NHBE cells, obtained from 4 different donor (Lonza), were genotyped to identify the presence of the TRPV1 SNP I585V. Of the 4 patient samples, 2 were heterozygous for the I585V SNP and 2 expressed WT TRPV1. These cells were plated in 12 well plates and treated with Coal Fly Ash (CFA) at multiple concentrations and capsasian. Differences between the patient samples were assessed.
2016-10-11 | GSE85447 | GEO
Project description:Gene expression was determined for normal human bronchial epithelial (NHBE) cells incubated with DMSO or TG immediately prior to infection with USSR H1N1 virus for 12 hours. All of the NHBE cell stocks were obtained from QIAGEN.
2020-10-02 | GSE120730 | GEO
Project description:Background and objective: Long term outcomes of allograft recipients are compromised by the development of chronic lung allograft dysfunction (CLAD) or bronchiolitis obliterans syndrome (BOS) which initiates in the lung periphery. We established baseline transcriptomic profiles of both the large and small airway epithelial cells (referred as LAEC and SAEC, respectively) to identify regional differences irrespective of initiating disease. Methods: We obtained matched primary LAEC and SAEC from lung allograft recipients (n=4, 42.5±4.2 years) and established primary cultures. Bulk RNA sequencing was performed to determine differentially expressed genes. Results: We observed differences in the transcriptional program between LAEC and SAEC Transcription factors (TF) were ranked within the top ten differentially regulated genes. The most abundant TF families included C2H2-ZF, homeobox and bHLH. Upstream regulator analyses identified homeobox genes being significantly in LAEC. Protein-protein interaction network analysis emphasised the role of TFs (ISL1, MSX1, HOXA1, GATA6, ZNF423) in airway modulation. Additionally, functional enrichment analysis revealed the activation of chemotaxis, metalloendipeptidase/metallopeptidase activity and pro-inflammatory signatures (IL17 signalling and RAGE), in LAEC, while SAEC were characterised by elevated expression of surfactant metabolism related genes. Moreover, alveolar and club cells-related genes were expressed in SAEC, suggesting a lower airway-specific signature. Conclusion: Our analysis shows robust transcriptional differences between LAEC and SAEC. We suggest a potential role for homeobox TF family as well as the activation of the immune system in the biology of LAEC. Conversely, we observed an alveoli-like transcriptional signature in SAEC, including gas-exchange signals and surfactant metabolism; pathways involved in lung homeostasis.
2022-10-01 | GSE214434 | GEO