This is so far the most significant genetic finding associated with AD. FLG is important for the structural SU5416 204005-46-9 integrity of the skin, and other functions are attributed to acidic degradation products of FLG, e.g. urocanic acid and pyrrolidone carboxylic acid. These are components of natural moisturizing factors and contributes to maintaining a low pH in the stratum corneum . In addition to FLG dysfunction, it has previously been demonstrated that the molecular background to the pathogenesis of AD is complex, and that several clusters of genes, including inflammatory and epidermal differentiation are altered in lesional AD skin. We set out to study whether the functional and molecular alterations in AD and IV skin depend directly on FLG loss-of-function variants, and whether the FLG genotype determine the type of downstream molecular pathways affected. Many of the potential AD candidate genes significantly altered in our study were located in chromosomal regions previously linked to AD , further highlighting these regions as interesting loci for potential candidate genes involved in AD susceptibility. The distributions of these differentially expressed genes in our study depended on FLG genotype, where several clusters were unique for each group, and others overlapped. Genes from these groups are mapped to significantly altered pathways in each patient group. The functional alterations evident from the significantly higher TEWL and pH such as inflammatory response following a more permeable barrier, as well as enzymatic activity where the pH level is important. The importance of changes in TEWL and pH has recently been highlighted in FLG deficient skin; where reduced levels of FLG degradation products are proposed to increase TEWL and pH; decreasing stratum corneum hydration and altering enzymatic activity. This may account for alterations in corneocyte and lipid organization within the SC. Given the frequent phenotypic overlap between dry skin, IV and AD; it is proposed that these functional alterations are important for the pathogenesis in both IV and AD skin with FLG deficiency. In support of this hypothesis, our AD patients without FLG mutations displayed lower functional barrier impairment measured by TEWL, lower pH and significantly lower mean SCORAD than AD patients with FLG mutations. In addition, the lowest number of significantly altered genes was detected in our AD FLG+/+ group. This suggests a correlation between number of affected genes, barrier impairment and disease severity among included AD patients. Of the many genes previously associated to AD several were also dysregulated in our array data, such as serine protease inhibitor kazal-type 5, mast cell chymase . Any discrepancies regarding expression of inflammatory mediators commonly found in AD may at least in part be due to lower expression of these genes in non-lesional skin. CD28 and STAT2 are two inflammatory markers that were confirmed to be altered also by qPCR.