A module-based approach to identify disease-relevant diagnostic and therapeutic candidate genes in allergy. (a) Twenty-five putative IL13-regulating transcription factors (TFs) were identified by combining data from mRNA microarrays, sequence-based predictions and the literature. (b) IL13-regulating TFs were validated by siRNA-mediated knockdown of the 25 TFs in human total CD4+ T cells polarized toward TH2 using IL13 as a read-out. The target genes of the TFs were identified by combined siRNA knockdown of the positively screened TFs/known IL13-regulating TFs from literature and microarray analyses. This resulted in a module of genes that was co-regulated with IL13 in TH2-polarized cells and significantly overlapped with differentially expressed genes from allergen-challenged T cells from allergic patients. For further validation experiments, the study focused on module genes that encoded secreted proteins and had not been previously associated with allergy. (c) Functional, diagnostic and therapeutic studies involving one of the module genes, S100A4, were performed in patients with seasonal allergic rhinitis, allergic dermatitis and a mouse model of allergy. (d) Model of S100A4-induced disease mechanisms. Allergic inflammation requires the sensitization of the immune system by allergens, resulting in the production of antigen-specific T cells. The interaction of dendritic cells (DC) in the draining lymph node with T cells is a critical step that is dependent on S100A4. B-cell maturation as a result of T cell-B cell crosstalk (for example, the release of TH2 cytokines by T cells) leads to the production of IgE and IgG1 by plasma cells. Cytokines and chemokines released by T cells stimulate the migration of circulating granulocytes (for example, neutrophils and eosinophils) to the inflammatory site (skin). Differentiation of naïve T cells into CD8+ cytotoxic T cells will exacerbate the skin damage. Blue arrows indicate the flow of the allergic responses. Green arrows indicate the promotion of these processes by S100A4. GEM, gene expression microarray.