ArticleJournal of cystic fibrosis : official journal of the European Cystic Fibrosis Society2019
RNA sequencing data from neutrophils of patients with cystic fibrosis reveals potential for developing biomarkers for pulmonary exacerbations.
Article in Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 28 citations in OpenAlex.
- Recent developments in cystic fibrosis drug discovery: where are we today?Expert opinion on drug discovery · 2025Review
- RNA Sequencing in Disease Diagnosis.Annual review of genomics and human genetics · 2024Review
- Diminished airway host innate response in people with cystic fibrosis who experience frequent pulmonary exacerbations.The European respiratory journal · 2024Article
- Whole blood transcriptomics reveals the enrichment of neutrophil activation pathways during erythema nodosum leprosum reaction.Frontiers in immunology · 2024Article
- Discovery of dysregulated circular RNAs in whole blood transcriptomes from cystic fibrosis patients - implication of a role for cellular senescence in cystic fibrosis.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2023Article
- CFTR-mediated monocyte/macrophage dysfunction revealed by cystic fibrosis proband-parent comparisons.JCI insight · 2022Article
- Sweat metabolomics before and after intravenous antibiotics for pulmonary exacerbation in people with cystic fibrosis.Respiratory medicine · 2022Article
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- Cystic Fibrosis: Systems Biology Analysis from Homozygous p.Phe508del Variant Patients' Samples Reveals Perturbations in Tissue-Specific Pathways.BioMed research international · 2021Article
- Evaluation of FGFR1 as a diagnostic biomarker for ovarian cancer using TCGA and GEO datasets.PeerJ · 2021Article
- Single-Cell Transcriptional Archetypes of Airway Inflammation in Cystic Fibrosis.American journal of respiratory and critical care medicine · 2020Article
- Whole-blood transcriptomic responses to lumacaftor/ivacaftor therapy in cystic fibrosis.Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society · 2020Article
- RNA Sequencing: A Potentiator of Discovery-based Research.American journal of respiratory cell and molecular biology · 2019Article
- Article
- Transcriptome Profiling and Molecular Therapeutic Advances in Cystic Fibrosis: Recent Insights.Genes · 2019Review
- Sputum Exosomal microRNAs Profiling Reveals Critical Pathways Modulated ByInternational journal of chronic obstructive pulmonary disease · 2019Article
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Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThere is no effective way to predict cystic fibrosis (CF) pulmonary exacerbations (CFPE) before they become symptomatic or to assess satisfactory treatment responses.
methodsRNA sequencing of peripheral blood neutrophils from CF patients before and after therapy for CFPE was used to create transcriptome profiles. Transcripts with an average transcripts per million (TPM) level > 1.0 and a false discovery rate (FDR) < 0.05 were used in a cosine K-nearest neighbor (KNN) model. Real time PCR was used to corroborate RNA sequencing expression differences in both neutrophils and whole blood samples from an independent cohort of CF patients. Furthermore, sandwich ELISA was conducted to assess plasma levels of MRP8/14 complexes in CF patients before and after therapy.
resultsWe found differential expression of 136 transcripts and 83 isoforms when we compared neutrophils from CF patients before and after therapy (>1.5 fold change, FDR-adjusted P < 0.05). The model was able to successfully separate CF flare samples from those taken from the same patients in convalescence with an accuracy of 0.75 in both the training and testing cohorts. Six differently expressed genes were confirmed by real time PCR using both isolated neutrophils and whole blood from an independent cohort of CF patients before and after therapy, even though levels of myeloid related protein MRP8/14 dimers in plasma of CF patients were essentially unchanged by therapy.
conclusionsOur findings demonstrate the potential of machine learning approaches for classifying disease states and thus developing sensitive biomarkers that can be used to monitor pulmonary disease activity in CF.
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