Ontology highlight
ABSTRACT:
PROVIDER: PRJNA437613 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6825510_1.fastq.gz | Fastqsanger.gz | |||
| SRR6825510_2.fastq.gz | Fastqsanger.gz | |||
| SRR6825520_1.fastq.gz | Fastqsanger.gz | |||
| SRR6825520_2.fastq.gz | Fastqsanger.gz | |||
| SRR6825530_1.fastq.gz | Fastqsanger.gz |
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Project description:Rationale: We recently demonstrated that the triple combination CFTR modulator therapy elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA) improves lung ventilation and airway mucus plugging determined by multiple-breath washout and magnetic resonance imaging in CF patients with at least one F508del allele. However, effects of ELX/TEZ/IVA on viscoelastic properties of airway mucus, chronic airway infection and inflammation have not been studied. Objectives: To examine the effects of ELX/TEZ/IVA on airway mucus rheology, microbiome and inflammation in CF patients with one or two F508del alleles aged 12 years and older. Methods: In this prospective observational study, we determined sputum rheology, microbiome, inflammation markers and proteome before and 1, 3 and 12 months after initiation of ELX/TEZ/IVA. Measurements and Main Results: CF patients with at least one F508del allele and healthy controls were enrolled in this study. ELX/TEZ/IVA improved the elastic and viscous modulus of CF sputum. Further, ELX/TEZ/IVA improved the microbiome α-diversity and decreased the relative abundance of Pseudomonas aeruginosa (P<0.05) in CF sputum. ELX/TEZ/IVA also reduced IL-8 and free NE activity, and shifted the CF sputum proteome towards healthy. Conclusions: Our data demonstrate that ELX/TEZ/IVA improves sputum viscoelastic properties, chronic airway infection and inflammation in CF patients with at least one F508del allele, however, without reaching levels close to healthy.
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Project description:Submucosal glands (SMGs) in the upper respiratory system of mammals play important roles in fluid secretion, mucociliary transport, and host defense. In people with cystic fibrosis (CF), airway mucus obstruction and SMG duct occlusion are hallmark features. Although intensive investigations have focused on airway surface epithelium in normal and diseased lungs, our knowledge of SMGs is limited in terms of cell biology and physiology. Here, we conducted single cell RNA sequencing (scRNA-seq) of airway SMGs in newborn piglets. First, we dissected individual SMGs and surrounding non-epithelial tissues from newborn non-CF (n = 4) and CF (n = 4) pig trachea. Second, we did scRNA-seq using 10x genomics chromium platform. Third, we processed the raw sequencing data using an improved RefSeq pig genome reference. Last, we integrated all samples together and clustered cells into 14 major cell clusters using Seurat R toolkit (Stuart et al., 2019). These data allowed us to elucidate airway SMGs at single cell resolution. Moreover, we found that cell-types and gene expression were the same in non-CF and CF SMGs, suggesting that loss of epithelial anion secretion rather than an intrinsic cell defect causes CF mucus abnormalities.
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Project description:Early life viral infections are responsible for pulmonary exacerbations that can contribute to disease progression in young children with CF. The most common respiratory viruses detected in the CF airway are human rhinoviruses (RV) and susceptibility to infection has been attributed to dysregulated airway epithelial responses, although evidence has been conflicting. Here, we exposed airway epithelial cells from children with and without CF to RV in vitro. Using RNA-Seq, we profiled the transcriptomic differences of CF and non-CF airway epithelial cells at baseline and in response to RV. There were only modest differences between CF and non-CF cells at baseline. In response to RV there were 1442 and 896 differentially expressed genes in CF and non-CF airway epithelial cells respectively. The core antiviral responses in CF and non-CF airway epithelial cells were mediated through interferon signaling although type 1 and 3 interferon proteins were reduced in CF airway epithelial cells following viral challenge consistent with previous reports. The transcriptional responses in CF airway epithelial cells were more complex than in non-CF airway epithelial cells with more over-represented biological pathways ranging from cytokine signaling to metabolic and biosynthetic pathways. Network analysis highlighted that the differentially expressed genes of CF airway epithelial cells transcriptional responses were highly interconnected and formed a more complex network than observed in non-CF airway epithelial cells. These data provide novel insights to the CF airway epithelial cells responses to RV infection and highlight potential pathways that could be targeted to improve antiviral and anti-inflammatory responses in CF.
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Project description:In this study, we assessed lower airway microbiome from a cohort of patients to determine whether specific microbiome taxa correlate with with specific metabolic activities. In a subset of 12 patients, transcriptomic expression were analyzed to compare host mucosa immune response We collected peripheral airway brushings from the 12 subjects whose lung microbiome were analyzed; Total RNA were obtained from the peripheral airway epithelium.
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