Fig. 3. Essential features of the tuft cell transcriptome are preserved after specific deletion of Ltc4s.

Tuft cells and epithelial cells were isolated from the naïve nasal mucosa of Chat^CretdTomato, Ltc4s^fl/fl, Chat^CretdTomatoLtc4s^fl/fl and Chat^CreLtc4s^fl/fl mice. Tuft cells were defined as EpCAM^highTomato⁺ in Chat^CretdTomato expressing mice and as EpCAM^highCD45^low in mice lacking the Tomato construct and were compared to EpCAM^highCD45⁻ and EpCAM^interm cells. (A) Expression of the tracheal scRNAseq signature (9) genes across tuft and non-tuft epithelial cells in the nose (expression level expressed as log2(TPM + 1). (B) Principal components analysis comparing each of the above populations of cells from Chat^CretdTomatoLtc4s^fl/fl, Chat^CreLtc4s^fl/fl and control Chat^CretdTomato and Ltc4s^fl/fl mice. (C) Volcano plot displaying significance (y axis, -log10(FDR)) of differential expression (x axis, log2 fold-change) in tuft cells derived fromChat^CretdTomato and Chat^CretdTomatoLtc4s^fl/fl mice. (D-E) Expression level of Ltc4s in tuft cells (D) derived from Ltc4s^fl/fl and Chat^CreLtc4s^fl/fl, Chat^CretdTomato and Chat^CretdTomatoLtc4s^fl/fl mice and macrophages (E) from Ltc4s^fl/fl and Chat^CreLtc4s^fl/fl mice. TPM counts derived from RNAseq analysis using DeSeq2. (F) In situ hybridization with RNAscope probe for Ltc4s (white). Tuft cells were distinguished based on immunoreactivity for advillin and neurogranin (magenta). Representative images of the trachea (top), and nose (bottom) of WT and Chat^CreLtc4s^fl/fl mice. (Scale bar: indicated in μm). (G) Heatmap of expression (log2(TPM+1), color bar) of genes in the lipoxygenase, cyclooxygenase pathway, Il25 and its receptor Il17rb expressed in nasal tuft cells and epithelial cells of the indicated genotypes. cKO, conditional knockout.