Granulocytes such as eosinophils are extremely difficult to functionally profile and are typically excluded from transcriptomic analyses due to their high RNase content. As such, there is a substantial knowledge gap surrounding the role of eosinophils in different tissues and disease states. Despite being destructive in diseases such as asthma, eosinophils have a protective role in the adipose tissue. This prompts the critical question: what genetic regulators switch eosinophils from being destructive to protective?
Using a highly optimised RNA extraction protocol and bioinformatic pipeline, we performed the first bulk RNA-seq of adipose-resident eosinophils. We found that adipose eosinophils are transcriptionally distinct from circulating eosinophils, with thousands of differentially expressed genes. Using epigenetic landscape in silico deletion analysis, we identified Activator Protein 1 (AP-1) and Krüppel-like factors (KLF) as key transcriptional regulators of the adipose eosinophil transcriptomic profile.
Next, we took a functional genomics approach, using CRISPR/Cas9 genome editing to individually knock-out the identified transcription factors in a human eosinophil cell line. RNA-seq and ChIP analysis revealed AP-1 member protein Activating Transcription Factor 3 (ATF3) as a key regulator of adipose eosinophil gene expression. Gene set enrichment analysis coupled with in vivo genetic mouse models has revealed that ATF3 regulates a fascinating new role for adipose eosinophils in the promotion of angiogenesis, a role we believe could become a compelling therapeutic target for obesity and metabolic disease.
These findings demonstrate the importance of performing functional genomic profiling of rare and challenging cell populations, as these studies can reveal unique tissue-specific roles that would otherwise be overlooked. Notably, these results highlight that tissue specialisation of cells is largely guided by genetic regulation at the transcriptional level.