CompareRhythms data in healthy and asthmatic airway epithelial cells

Rationale: Cellular circadian rhythms regulate multiple cellular processes and have been hypothesized to influence epithelial function in asthma. Airway resistance has circadian variability in patients with asthma, profiling of circadian rhythms of gene expression in human airway epithelia has not been performed. Organotypic cultures of primary human airway epithelial cells differentiated at an air-liquid interface recapitulate the major cell types of human airway epithelia to allow for evaluation of gene expression not possible in vivo and demonstrate rhythmicity of core circadian genes after temperature synchronization.

Methods:  Primary human airway epithelial cells from 6 healthy children and 6 children with asthma were differentiated an air-liquid interface and circadian rhythms were synchronized using cycled incubator temperature. RNA was harvested every 4 hours and RNA-sequencing performed to measure transcriptome-wide expression, with differential rhythmicity of genes identified using CompareRhythms.

Results: Core circadian genes ARNTL and NR1D1 demonstrated rhythmicity in both healthy and asthmatic airway epithelial cells with maintained phase relationships. In RNAseq data from healthy and asthmatic airway epithelial cells, 646 (4%) of protein-coding genes were rhythmic, with 110 genes exhibiting differential rhythmicity in asthma. Gene set enrichment analysis using EnrichR revealed that genes in circadian rhythm, nuclear receptor, and cell adhesion pathways were rhythmic. Neutrophil chemotaxis, cytokine mediated signaling, and viral protein interactions with cytokine receptor pathways demonstrated differential (gain, loss, or change) rhythmicity in asthma.

Conclusions: Core circadian rhythm genes maintain rhythmicity in healthy and asthmatic human airway epithelia, and regulate cytokine mediated signaling and neutrophil chemotaxis pathways in asthmatic human airway epithelia.

Methods
AECs from healthy children and children with physician-diagnosed allergic asthma were obtained from subjects (ages 6-16) while under general anesthesia for elective procedures. AECs were expanded and at passage 3 were differentiated at an ALI in PneumaCult ALI media (Stemcell) at 37°C, producing an organotypic differentiated epithelial culture with mucociliary morphology. AECs from children were obtained under study #12490 and #1596 approved by the Seattle Children’s Hospital Institutional Review Board with investigations conducted following the rules of the Declaration of Helsinki of 1975. Temperature cycled synchronization occurred for 6 days (12 hours at 37°C, 12 hours at 34°C), then cultures were maintained at a constant 37°C for 48 hours during RNA isolation. RNA was collected every 4 hours for 48 hours, beginning 4 hours after final media change and completion of temperature synchronization. Two independent cultures were harvested for RNA at each timepoint. Samples with RIN >8 were prepared using poly-A library preparation by Novogene sequencing using 150 base paired-end reads with targeting 20-30 million reads per sample performed using Illumina sequencing. STAR (version 2.4.2a) was used to align reads after adapter trimming to the Ensembl version of the human genome (GRCh38, Ensembl 91). For quality control, samples that had human aligned counts greater than 5 million mapped reads and a median coefficient of variation coverage less than 0.9 were kept. No samples failed quality control. Genes were filtered to include those that had at least 0.1 counts per million in at least 40 samples and further filtered for protein coding genes. Counts were then normalized using the trimmed mean of M (TMM) approach in the edgeR package. In R, the package CompareRhythms using the cosinor function was used to characterize rhythmicity with FDR adjusted p-value of 0.05, minimum amplitude 0.2, period length of 24, and an FDR cutoff of 0.2 for differential rhythmicity.