Expression profile and identification of DEGs between patients with ATA and those with AERD
From the 10 asthmatic patients collected, the average 35,160,551 pairs of RNA-seq per sample was produced, and 35,115,725 pairs (7,039,115,605 bp) were presented after the adapter and low quality trimming (Table S1). Gene expression profiling was conducted by reads mapping against the human reference genome (hg19), and the normalization and sample clustering was attempted to compare between the AERD and ATA groups (Figure 1A and Table S2).
DEGs were selected according to aspirin intolerance, adjusting with atopy status. Under the criteria of P value < 0.05 and logFC ≥ |1|; we found 1,736 DEGs: 832 were up-regulated and 904 were down-regulated in patients with AERD (Figure 1, B and C).
Estimation of methylation levels and D ifferentiallyM ethylated R egions (DMRs)
The number of statistically significant CpGs from the chip was 865,912 at the P value < 0.01 and 865,917 at the P value < 0.05. Of the total samples (10 patients), CpG sites whose uncertain methylation values were greater than 25% in the sum of NA, and P values > 0.05 were excluded from further analysis. The remaining 865,384 CpGs after the filtering were used for subsequent analysis.
The DNA methylation profile was generated in 10 asthmatics. After adjusting for atopy status, we found 1,401 DMPs using ChAMP (R-package for methylation analysis pipeline): 13 with higher methylation and 1,388 with lower methylation in patients with AERD (Figure 2A and Table S3). As shown above, the genomic distribution of extracted DMPs was confirmed at the significance level of P value and the condition of aspirin intolerance. Most DMPs from AERD and ATA were frequently observed at the upstream regulatory region, such as TSS, UTR, and 1st Exon, according to the ratio of the region occupied by whole genome (Figure 2B), suggesting that methylation changes occur primarily in the regulatory domain.