Stem cells or inner bulge niche cells were isolated from Sox9CreER cKO or matched littermate heterozygous control animals, that were either treated with low-dose Tamoxifen (Tamlow, to target only the inner bulge niche cells for Cdh1 loss-of-function) or regular-dose Tamoxifen (Tamreg, to target both inner bulge niche and stem cells). (A) KEGG pathway analyses of genes significantly up-regulated (p < 0.05, absolute fold-change ≥1.5) in Cdh1-null vs control inner bulge niche cells (both with normal stem cells). Shown are the top 10 of 30 pathways with p-values<0.05. (B) KEGG pathway analyses of genes significantly up-regulated (p < 0.05, absolute fold-change ≥1.5) in Cdh1-null vs control HF stem cells (HFSCs) from Cdh1-null or control bulge. Shown are the top 10 of 50 pathways with p-values<0.05. Overall, p-values are much lower for stem cells than inner bulge niche cells (A). (C) Fold-changes (FC) of significantly up-regulated genes in Cdh1-null stem cells from Cdh1-null bulge. Listed at right are top genes associated with immune response (FCs indicated in parentheses). (D) Top, Venn diagram comparing changed transcripts in WT stem cells that surround either a Cdh1-null mutant inner bulge niche (Tamlow) or a WT inner bulge niche (no Tam). Both populations commonly express 13208 genes (TPM [transcripts per kilobase million]≥1), but WT stem cells surrounding a mutant inner bulge gain expression of 1365 genes by ≥1.5 fold and lose expression of 1027 genes (TPM <1). Bottom, Venn diagram comparing gene expression changes in stem cells vs inner bulge niche cells from Cdh1-null bulge. Note that the stem cells and their niche adopt highly distinct transcriptomes (upregulated genes shown here). (E) Principal component analysis (PCA) comparing transcriptomes of telogen-phase HF stem cells of WT, Cdh1 cKO and Het bulges, and of anagen II/III HF stem cells from WT bulges. (F, G) Relative expression of genes within the KEGG pathway term ‘cytokine-cytokine receptor interaction’ and genes associated with immune response that scored as significantly up-regulated (Cdh1-null vs control) for niche (F) or stem cells (G). Note that of the few immune signaling genes in the breached niche signature, most are more highly and significantly expressed by the stem cells (*) (F); conversely, many immune response genes in the stem cell signature are barely expressed, if at all, in the breached inner bulge niche (G). Navy and red bars correspond to data from Tamreg mice; orange, black and brown bars correspond to data from Tamlow mice. (H) Two highly upregulated immune response stem cell genes, Ccl1 and Ccl2, are still as highly expressed even after antibiotics treatment, underscoring their independence from bacterial infiltration. qRT-PCR data are normalized to Ppib. Data are mean ±SEM (n = 4 mice per condition/genotype). ns, non-significant. All data were from Tamreg mice. (I, J) Transwell migration assays. Cdh1-null and Ctrl HF stem cells were seeded in bottom Boyden chamber. Bone marrow-derived dendritic cells (BMDCs) or macrophages (BMDM), either WT or deficient for CCR2 receptor, were placed in upper chamber, with or without isotype control or CCR8 blocking antibody. CD45+ BMDCs and BMDM that were chemo-attracted to bottom chambers were quantified by flow cytometry. Data are mean ±SEM (n = 3). Comparisons that are statistically significant are denoted by asterisks. *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001.