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Inflammatory bowel disease (IBD) is assumed to be caused by genetic and environmental factors that interact together in promoting intestinal immune dysregulation where cytokines have validated role. However, the underlying intimate mechanisms in the human IBD involving cytokines still needs to be supplemented especially in the clinical context. The aim of this study was to investigate the expression of some inflammatory and regulatory cytokines (IL-17A, IL-23, IL-6, TGFβ1, and IL-10) as well as of the transcription factor FoxP3 in mucosal samples of IBD and non-IBD patients. We assessed the mRNA relative quantities (RQ) of the above-mentioned cytokines and the transcription factor FoxP3 in paired colonic samples (inflamed and adjacent normal mucosa) from 37 patients with IBD and in normal mucosal tissue in 12 persons without IBD by performing a qRT-PCR assay and tested the protein levels of target cytokines in serum samples. The patients were divided into three groups: without any therapy (n = 10), on 5-ASA (n = 11) and on immunosuppressants (Azathioprine ± 5-ASA/corticosteroids) (n = 16) in order to compare the RQ values for each therapeutic group. All investigated genes were found upregulated in the inflamed mucosa of IBD patients in the following order: IL-6 > FoxP3 > TGFβ1 > IL-23 > IL-17A > IL-10. We also observed that the gene expression of FoxP3 and IL-6 were substantially higher in the inflamed mucosal tissue of the IBD patients than the adjacent normal mucosa (p = 0.035, p = 0.03 respectively). Differences between higher mRNA expression of FoxP3 and IL-6 in inflamed tissue were considered significant in patients with ulcerative colitis (UC) (p = 0.011, p = 0.000 respectively) and with Crohn’s disease (CD) (p = 0.008, p = 0.000 respectively) in comparison to the normal mucosa of non-IBD persons and we found increased TGFβ1 in CD patients alone (p = 0.041). Furthermore, IL-6 and TGFβ1 were overexpressed (RQ > 10) in non-inflamed mucosa from IBD patients compared to the normal mucosa from the controls. When we compared the gene expression for paired mucosa in the immunosuppressive treated group with the 5-ASA treated group we observed opposite changes in IL-6 and TGFβ1 expression. Additionally, we found higher serum levels of IL-23 (p = 0.008), TGFβ1 and IL-6 in IBD patients compared to non-IBD patients. The obtained specific expression profile consisting of IL-6, TGFβ1, IL-10 and FoxP3 may represent a transcriptional hallmark for IBD. Furthermore, we found that treatment with immunosuppressive therapy was more beneficial for driving cytokine expression to restore immune regulation in patients with IBD, unlike the 5-ASA therapy. [ABSTRACT FROM AUTHOR]