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Previous studies have demonstrated that<jats:italic>A. fumigatus<\/jats:italic>conidia are internalized by macrophages and lung epithelial cells; however the exact transcriptional responses of airway epithelial cells to conidia are currently unknown. Thus, the aim of this study was to determine the transcriptomic response of the human bronchial epithelial cell line (16HBE14o-) following interaction with<jats:italic>A. fumigatus<\/jats:italic>conidia. We used fluorescence-activated cell sorting (FACS) to separate 16HBE14o- cells having bound and\/or internalized<jats:italic>A. fumigatus<\/jats:italic>conidia expressing green fluorescent protein from cells without spores. Total RNA was then isolated and the transcriptome of 16HBE14o- cells was evaluated using Agilent Whole Human Genome microarrays.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Immunofluorescent staining and nystatin protection assays demonstrated that 16HBE14o- cells internalized 30-50% of bound conidia within six hrs of co-incubation. After FAC-sorting of the same cell culture to separate cells associated with conidia from those without conidia, genome-wide analysis revealed a set of 889 genes showing differential expression in cells with conidia. Specifically, these 16HBE14o- cells had increased levels of transcripts from genes associated with repair and inflammatory processes (<jats:italic>e.g.<\/jats:italic>, matrix metalloproteinases, chemokines, and glutathione S-transferase). In addition, the differentially expressed genes were significantly enriched for Gene Ontology terms including: chromatin assembly, G-protein-coupled receptor binding, chemokine activity, and glutathione metabolic process (up-regulated); cell cycle phase, mitosis, and intracellular organelle (down-regulated).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We demonstrate a methodology using FACs for analyzing the transcriptome of infected and uninfected cells from the same cell population that will provide a framework for future characterization of the specific interactions between pathogens such as<jats:italic>A. fumigatus<\/jats:italic>with human cells derived from individuals with or without underlying disease susceptibility.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2164-11-358","type":"journal-article","created":{"date-parts":[[2010,6,5]],"date-time":"2010-06-05T06:13:50Z","timestamp":1275718430000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":48,"title":["Functional genomics of human bronchial epithelial cells directly interacting with conidia of Aspergillus fumigatus"],"prefix":"10.1186","volume":"11","author":[{"given":"Pol","family":"Gomez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tillie L","family":"Hackett","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margo M","family":"Moore","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Darryl A","family":"Knight","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott J","family":"Tebbutt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2010,6,4]]},"reference":[{"issue":"9","key":"2952_CR1","doi-asserted-by":"publisher","first-page":"4101","DOI":"10.1128\/JCM.41.9.4101-4106.2003","volume":"41","author":"A Warris","year":"2003","unstructured":"Warris A, Klaassen CH, Meis JF, De Ruiter MT, De Valk HA, Abrahamsen TG, Gaustad P, Verweij PE: Molecular epidemiology of Aspergillus fumigatus isolates recovered from water, air, and patients shows two clusters of genetically distinct strains. 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