Unknown,Transcriptomics,Genomics,Proteomics

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Bulk RNA Barcoding and sequencing (BRB-seq) of Mock, ICV, and IDV infected airway epithelial cell cultures of human, porcine, and bovine origin at 33°C and 37°C

ABSTRACT: For the assessment of host response dynamics to ICV and IDV infections in human, porcine, and bovine airway epithelial cells at ambient temperature corresponding to the upper or lower respiratory tract. We performed a temporal transcriptome analysis on human, porcine, and bovine airway epithelial cell (AEC) cultures infected with ICV and IDV, as well as uninfected hAEC cultures, incubated either at 33°C or 37°C. AEC cultures from the different species were harvested at 24, 48 72, 96 hpi and processed for Bulk RNA Barcoding and sequencing (BRB-seq), which allows a rapid and sensitive genome-wide transcriptomic analysis in a highly multiplexed manner. Transcriptome data from human, procine, and bovine was obtained from a total of 3 biological donors for pairwise comparisons of ICV and IDV virus-infected to unexposed AEC cultures at respective time points and temperatures.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Sus scrofa

SUBMITTER: Ronald Dijkman

PROVIDER: E-MTAB-11939 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: Basal cells within the human airway epithelium constitute the stem/progenitor cells for other epithelial cell types. Basal cells respond to mucosal injury and damage to the airway mucosa in an ordered sequence of spreading, migration, proliferation and phenotype shifting (differentiation) to other needed cell types. However, dynamic gene transcription in the early events of injury and repair has not been examined in these cells. Methodology and findings: Airway epithelial cells were obtained from donated lungs and grown in submersion culture on pliable membranes to obtain a pure population of basal cells. Microarrays were used to assess the transcriptome of basal cells 8 and 24 hr after mechanical injury (MI), or to cyclic stretch (CS) in a Flexcell system (0.5 Hz, 20% distension), or both treatments. We identified 121 signature genes with > 2-fold higher differential expression (DE) 8 hr after MI; expression of nearly all of these genes returned to baseline at 24 hr after injury. In cells subjected to CS, little change in DE was noted at 8 hr, whereas at 24 hr a CS signature of 1430 DE genes were identified. The MI signature was characterized by genes encoding growth factor receptors related to the EGF pathway, IL-6, IL-8 and IL-33, extracellular matrix components, and NF-kB and p38-MAPK signaling pathways, whereas the CS signature was characterized by a broad range of genes that did not identify specific signaling pathways. Combined MI and CS at 8 hr elicited DE of down-regulated genes not seen with either stimulus alone, and at 24 hr elicited DE that was similar to that seen with CS alone. Conclusion and significance: The human airway basal epithelial cell transcription signature in the first hours after MI, after CS, and after both stimuli identifies unique differentially expressed genes and pathways that may be important in the early molecular response and biology to airway injury. Total RNA obtained from primary (AEC) and differentiated (dAEC) human airway epithelial cells subjected to 8 or 24 hours in vitro mechanical or cyclic stretch or both injuries compared to sham control as well as to type of injury. Cells were collected from four donated lungs and cultured separated in submission or air liquid interface condition prior to injury for various durations.

Dataset Information

Bulk RNA Barcoding and sequencing (BRB-seq) of Mock, ICV, and IDV infected airway epithelial cell cultures of human, porcine, and bovine origin at 33°C and 37°C

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