METHODS: Using data from GSE55385, GSE43660, GSE56292, and GSE69707 and the BioWardrobe platform, we analyzed differential gene expression between mouse genetic strains, tissue origin of the eosinophils (BM or lung), and eosinophil derivation (native eosinophils or cultured eosinophils).
RESULTS: When searching “eosinophil(s)” in the Gene Expression Omnibus (GEO) repository, only four DataSets included RNA sequencing from homeostatic murine eosinophils. A high proportion (> 90%) of genes share expression between BALB/c and C57BL6/J BM eosinophils. Seventy-seven percent of genes were differentially expressed ( ³ 2 fold, P < 0.01) between lung-resident and BM eosinophils. Notably, eosinophils cultured from BM cells have a significantly higher expression level for more than 50% genes than do native eosinophils.
CONCLUSIONS: The eosinophil transcriptome from culture-derived eosinophils is markedly different than that from native BM eosinophils. In addition, the local tissue environment impacts gene expression in eosinophils to a much greater extent than does genetic background at homeostasis. Although eosinophils are highly under-represented in the GEO repository, our study is the first to highlight the value of reusing public expression data for eosinophil research and the affect of local environmental signals on gene expression in eosinophils at homeostasis.