PIAMA nasal RNAseq data
Ontology highlight
ABSTRACT:
PROVIDER: EGAS00001006240 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This study included nasal gene expression data collected from nasal brushes of adolescents in PIAMA birth cohort, which is used in the project Nasal DNA methylation at three CpG sites predicts childhood allergic disease. 186 samples were included in this analysis, and phenotypes (age and sex) were provided together with a gene expression count table. Gene expression was measured by the Illumina HiSeq2500 sequencer.
| EGAD00001008767 | EGA
Project description:Genome wide DNA methylation profiling of nasal-epithelial swabs collected from vaping and non-vaping (within 6 months) adolescents from Denver, Aurora, and Pueblo, CO . The Illumina Infinium Human Methylation 850K beadchip profiling microarray was used to obtain DNA methylation profiles across approximately 868,000 CpGs. Samples included 11 swabs from adolescents who had vaped in the last 6 months, and 37 who had not.
2024-07-05 | GSE240130 | GEO
Project description:Electronic cigarette use (vaping) among adolescents is a pressing public health issue. We aimed to investigate the impact of vape use on lung function and nasal epithelial gene expression in adolescents. We hypothesized that vaping results in abnormal lung function and differential expression of inflammatory genes in the nasal epithelium of adolescent vape users in comparison to non-vape users. We assessed airflow obstruction with impulse oscillometry (IOS) and collected nasal epithelial brush samples for genome-wide gene expression and targeted DNA methylation analyses in middle and high school students in Colorado. Written informed consent was obtained from participants and Institutional Review Board approval was obtained. Vape users [mean age (standard deviation): 14.8 (1.4) years] reported vaping within the past 6 months while non-vape users [14.8 (1.4)] years did not report any vape use in the past 6 months. Mean airway resistance identified by the IOS R5 measure revealed that vape users (n=13) had higher values than non-vape users (n=37) [p=0.026]. Of 16,860 nasal epithelial genes tested, 7,136 were significantly differentially expressed between vape and non-vape users (false discovery rate (FDR) <0.05), after covariate adjustment. Enrichment analyses identified overexpression of inflammatory response genes and underexpression of ciliogenesis genes in vape users compared to non-vape users. DNA methylation analysis revealed that REXO1 (FDR=0.01) and CERK (FDR=0.06) were differentially methylated among vape users compared to non-vape users. Vaping during adolescence may increase airway resistance and dysresgulation of nasal epithelial genes, including genes involved in airway inflammation and ciliary function.
2024-07-05 | GSE238235 | GEO
Project description:NSAID-exacerbated respiratory disease (N-ERD) represents a particularly severe endotype of chronic rhinosinusitis with nasal polyps (CRSwNP), which affects around 10-16% of CRSwNP patients. N-ERD is characterized by severe and refractory nasal polyposis, bronchial asthma and intolerance to non-steroidal anti-inflammatory drugs (NSAIDs), including aspirin. Today, the pathogenesis of N-ERD remains incompletely understood and curative treatments are lacking. Using a global transcriptomic approach, we identified local changes between the mucosa of N-ERD nasal polyps and healthy control inferior turbinates. Nasal brushing samples were collected from inferior turbinates of healthy controls and nasal polyps of N-ERD patients under anterior rhinoscopy and stored at -80°C in RNAprotect until RNA isolation and RNAseq.
2020-06-30 | E-MTAB-7962 | biostudies-arrayexpress
Project description:We report the analysis of nasal curettage cells by RNAseq collected at pre-symptomatic timepoints in healthy adults experimentally challenged with respiratory syncytial virus (RSV). Following inoculation, 57% of participants developed PCR-confirmed infection. Prior to viral challenge, 80 differentially expressed genes were identified that associated with susceptibility to symptomatic infection. At day 3, 87 differentially expressed genes were associated with protection. Thus, we showed that the nasal mucosa at the time of virus exposure and during the incubation phase correlate with susceptibiltiy and protection from respiratory viral infection.
2020-09-01 | GSE155237 | GEO
Project description:We previously derived and validated a bronchial epithelial gene expression biomarker to detect lung cancer in current and former smokers. Given that bronchial and nasal epithelium gene expression is similarly altered by cigarette smoke exposure, we sought to determine if cancer-associated gene expression might also be detectable in more readily accessible nasal epithelium. Nasal epithelial brushings were prospectively collected from current and former smokers with pulmonary lesions suspicious for lung cancer in the AEGIS-1 (n=375) and AEGIS-2 (n=130) clinical trials and gene expression profiled using microarrays. Using the 375 AEGIS 1 samples, we identified 535 genes that were differentially expressed in the nasal epithelium of patients who were ultimately diagnosed with lung cancer vs. those with benign disease after one year of follow-up (p<0.001). Using bronchial gene expression data from 299 AEGIS-1 patients (including 157 patients with matched nasal and bronchial expression data), we found significantly concordant cancer-associated gene expression differences between the two airway sites (p<0.001). Differentially expressed genes were enriched for genes associated with the regulation of apoptosis, mitotic cell cycle, and immune system signaling. A nasal lung cancer classifier derived in the AEGIS-1 cohort that combined clinical factors and nasal gene expression had significantly higher AUC (0.80) and sensitivity (0.94) over a clinical-factor only model (p<0.05) in independent samples from the AEGIS-2 cohort (n=130). These results suggest that the airway epithelial field of lung cancer-associated injury in current and former smokers extends to the nose and demonstrates the potential of using nasal gene expression as a non-invasive biomarker for the detection of lung cancer.
2017-06-27 | GSE80796 | GEO
Project description:Purpose: Choline acetyltransferase (ChAT)-expressing epithelial cells are found in the upper and lower airways. In the trachea, they are referred to as brush cells. In the mouse nose two distinct populations of ChAT-eGFP+ cells had been previously described: a population of rare solitary chemosensory cells (SCCs) in the respiratory mucosa and a more abundant population of microvillous cells (MVCs) in the olfactory epithelium. Besides ChAT expression, SCCs share the expression of bitter taste receptors and signaling machinery with tracheal brush cells as well as close association with CGPR+ nerve fibers and an elongated shape. MVCs do not express bitter taste receptors, are not clearly associated with nerves and are smaller in size than SCCs. We have previously reported the transcriptional profile of tracheal ChAT-expressing brush cells but the transcriptional profile of nasal chemosensory ChAT+ epithelial cells has not been reported. Methods: In this study, we isolated nasal ChAT-eGFP+ cells by FACS from naïve ChAT(BAC)-eGFP mice with knockin of eGFP within a BAC spanning the ChAT locus, marking brush cells in the epithelium and performed transcriptome profiling using low input RNA sequencing. We sorted two distinct subsets of ChAT-eGFP+ epithelial cells from the nasal mucosa based on FACS ice and granularity characteristic: ChAT-eGFP+ EpCAM+ FSC/SSChigh (representing 5% of all ChAT-eGFP+ cells) and FSC/SSClow (representing 95% of all ChAT-eGFP+ cells), respectively. We compared them to unfractionated ChAT-eGFP- EpCAM+ epithelial cells. Results: Both nasal ChAT-eGFP subsets shared the core transcriptional profile of chemosensory cells from the intestine, trachea, gallbladder and thymus including the expression of Il25, Pou2f3, Trpm5, Avil, Plcb2 and transcripts of eicosanoid biosynthetic enzymes suggesting that most ChAT-eGFP+ cells in the nose belong to the chemosensory/tuft/brush cel family. The two subsets of nasal ChAT-eGFP+ cells differed in expression of taste receptors and taste receptor signaling machinery. Conclusions: Our study represents the first detailed analysis of the transcriptome of nasal ChAT-eGFP+ cells (brush cells) and identifies two subsets of nasal brush cells that share a core transcriptional signature but differ in expression of bitter taste receptors.
2020-01-16 | GSE139014 | GEO
Project description:Nasal Microbiome Diversity: Insights and Implications from a Lithuanian Cohort Study
| PRJEB70777 | ENA
Project description:mRNA expression was assayed from bronchial epithelial cells collected via bronchoscopy and nasal epithelial cells collected by brushing the inferior turbinate from healthy current and never smoker volunteers in order to determine the relationship between smoking-related gene expression changes in bronchial and nasal epithelium within the same individual.
2011-03-14 | GSE16008 | GEO
Project description:Background: Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development. Objective: We hypothesized that children raised in farm environments have a lower incidence of viral illnesses over the first two years of life than non-farm children. We also analyzed between farm exposures or respiratory illnesses were related to patterns of nasal cell gene expression. Methods: The Wisconsin Infant Study Cohort (WISC) birth cohort enrolled farm and non-farm pregnant women from central Wisconsin. Parents reported prenatal farm and other environmental exposures. Illness frequency and severity were assessed using illness diaries and periodic surveys. Nasopharyngeal cell gene expression at age two years was compared to farm exposure and respiratory illness history. Results: There was a higher rate of respiratory illnesses in the non-farm vs. farm group (rate ratio 0.82 [0.69,0.97], p=0.020), but no significant differences in wheezing illnesses. There was a stepwise reduction in rates of respiratory illnesses in children exposed at least weekly to 0, 1, or ≥2 animals (p=0.006). In analyzing nasal cell gene expression, farm exposures and preceding respiratory illnesses were positively related to gene signatures for mononuclear cells and innate and antimicrobial responses. Conclusions: Children exposed to farms and farm animals had lower rates of respiratory illnesses over the first two years of life. Both farm exposures and preceding respiratory illnesses were associated with increased innate immune responses, suggesting that these exposures stimulate mucosal immune responses to reduce subsequent illness frequency.
2024-01-29 | GSE233761 | GEO