GSE196550
Analysis of HOIL1-dependent gene expression in the murine small intestine
The goal of this study was to examine the role of HOIL1 in regulating gene expression in the small intestine. Using histological and qRT-PCR analyses, we had identified type 2 inflammation, including excessive expression of Il13, Il5 and IL-4 mRNAs, in the ileum of HOIL1-deficient mice. To determine the mechanism by which HOIL1 regulates type 2 inflammation, we performed RNA-seq to identify additional transcriptional changes. Since IL-13/IL-4 signaling in intestinal epithelial cells (IECs) triggers extensive changes in the cell-type composition and expression in the epithelial layer that further promotes type 2 inflammation, we deleted the IL-4Ralpha on IECs by crossing Hoil1 mutant mice to Il4ra-floxed and Vil1cre transgenic mice to block feed-forward signaling and epithelial changes. We FACS-sorted CD45-positive and CD45-negative cells from the ileum of these mice to increase the sensitivity of detection of mRNA changes in each of these populations. In the preliminary analyses of these data, we filtered the data to identify transcriptional changes that were dependent on HOIL1, but independent of IL4Ralpha signaling on IECs. Six transcripts, in addition to Rbck1 (official gene name for Hoil1), were identified as differentially expressed (DE) in the CD45-positive population. All six genes have been previously associated with group 2 innate lymphoid cells and/or Th2 cells. Only Rbck1 was identified as DE in the CD45-negative population under these criteria. Overall design: mRNA profiles of CD45-positive and CD45-negative cells isolated from the small intestine of Hoil1+/+Il4raflox/flox, Hoil1+/+Il4raflox/flox+Vil1cre, Hoil1-/-Il4raflox/flox, and Hoil1-/-Il4raflox/flox+Vil1cre mice (Peyer's patches removed).