Tape-strips and biopsies capture key AD-related immune alterations
Using FCH≥2 and FDR<0.05 criteria, tape-strips and biopsies, respectively, detected 4,104 (2,513 Up; 1,591 Down) and 1,273 (546 Up; 727 Down) DEGs in AD versus controls (Figure 1B ). The common phenotype between tape-strip and biopsy groups comprised of 536 DEGs (310 Up; 226 Down).42 The tape-strip group had 3,568 unique DEGs (2,203 Up; 1,365 Down), whereas biopsies had 737 unique DEGs (230 Up; 292 Down) as depicted in the Venn diagram in Figure 1B .
Using a previously published immune-data set,17,29,42-46 we identified inflammatory genes that were differentially expressed in AD versus controls in at least one comparison (Figure 2, Table E1 ). The immune-related DEGs with the highest FCHs are shown in a heatmap in Figure 2A-B and a visual word cloud of representative immune markers, where the size of the letters represents the magnitude of the FCHs in AD versus healthy skin, is depicted in Figure 2C-D . Both tape-strips and biopsies showed significant up-regulation in key products involved in general inflammation (MMP12), innate immunity (IL-6), T-cells/T-cell activation (CD2, CD3D/E/G, CD4, CD5, CD28, ICOS, GZMA), dendritic cell (DC) activation and migration (FCER1G, ITGAM/CD11B, ITGAX/CD11C, CD80, CXCR4), regulatory markers (IL-10, CTLA4, FOXP3, CD274), Th2 (IL-13, CCL13, CCL17, CCL18, CCL22, IL-4R, TNFRSF4/OX40, OSM, CCR4), Th1 (IL-12B, CXCL9, CXCL10, MX1, OASL), Th17 (CCL20, CXCL1, IL-19, IL-20, IL-36A, PI3), and antimicrobial peptides (CAMP/LL37) (Figure 2, Table E1 ). Both techniques also demonstrated significant down-regulation of negative regulators IL-34, IL-37, IL-1F10. These markers all notably showed greater FCHs in tape-strips than in biopsies, particularly for select markers of T-cells/T-cell activation (CD3D, CD3E, GZMA), negative regulation (CD274, IL-34), DC activation and migration (FCER1G, CD80, ITGAM/CD11B, ITGAX/CD11C, CXCR4), and Th2 (IL-13, CCL17, TNFRSF4/OX40, CCR4, OSM), where the FCHs between AD and controls were at least 5-fold in tape-strips compared to biopsies (Figure 2A and C ). Moreover, multiple additional genes involved in innate immunity or general immune activation (IL-1B, IL-8, PDE4A, PDE4B, PTPRC, NLRP3, TLR4), tissue resident memory T-cells (CD69), DCs (CD83, CD86, CD1A, CD1C, CD1E, FCER1A, CD207/langerin, IL-3RA, IRF4),9,47,48 macrophages (RNASE1, MS4A4A, F13A1, CECR1), Th1/Th2 (CCL3), and Th17 (CXCL2, CXCL3, GPR183, TGM2, DUSP4) were uniquely up-regulated in tape-strips, but not biopsies (Figure 2, E1,Table E1 ). Conversely, the Th1-defining cytokine IFN-γ, CCL26, a Th2 chemokine, and CCL19, a chemokine involved in T-cell trafficking, were uniquely significantly up-regulated in biopsies. Th22 and Th17/Th22-related genes (IL-22, IL-26, S100A7, S100A8, S100A9, DEFB4B, and LCN2) showed higher or unique up-regulation in biopsies compared to tape-strips. Collagens (COL6A5, COL6A6, TNC) implicated in driving AD inflammation were also uniquely up-regulated in biopsies (Figure E1, Table E1 ).9