IRF5 genetic risk variants drive myeloid-specific IRF5 hyper-activation and pre-symptomatic SLE

The IRF5-SLE risk haplotype is associated with SLE disease severity. We hypothesized that neutrophils from healthy risk donors would carry a pathogenic gene signature compared to non-risk donors. To compare basal neutrophil gene signature between risk and non-risk healthy individuals, fresh whole blood was collected from healthy donors, and granulocytes were extracted from the remaining pellet following Ficoll purification. RNA-seq libraries were prepared from globin-reduced RNA extracted from the granulocytes using the Qiagen RNA preparation kit. Neutrophils from healthy donors with the IRF5-SLE risk haplotype (n=6) and with a non-risk IRF5-SLE haplotype (n=8) were extracted from whole blood for RNA-sequencing. Quality filters were applied to exclude samples with fewer than 4 million total reads, a median CV of coverage greater than 50%, or less than 75% alignment to the reference genome. An additional library was excluded due to outlying quality variance identified by PCA. Following this quality control, 11 of 14 samples (5 risk and 6 non-risk) remained for downstream analysis.