In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells

The performance of linear and quadratic discriminant analysis (LDA, QDA) in identifying NF-κB-responding genes was examined on a dataset of 240 positive and negative examples of NF-κB regulation, using stratified cross-validation with an internal leave-one-out cross-validation (LOOCV) loop for automated feature selection and noise reduction. LDA performed slightly better than QDA, achieving 61% sensitivity, 91% specificity and 87% positive predictive value, and allowing the identification of 231, 251 and 580 NF-κB putative target genes in insulin-producing INS-1E cells, primary rat beta-cells and human pancreatic islets, respectively. Predicted NF-κB targets had a significant enrichment in genes regulated by cytokines (IL-1β or IL-1β + IFN-γ) and double stranded RNA (dsRNA), as compared to genes not regulated by these NF-κB-dependent stimuli. We increased the confidence of the predictions by selecting only evolutionary stable genes, i.e. genes with homologs predicted as NF-κB targets in rat, mouse, human and chimpanzee.The present in silico analysis allowed us to identify novel regulatory targets of NF-κB using a supervised classification method based on putative binding motifs. This provides new insights into the gene networks regulating cytokine-induced beta-cell dysfunction and death.Pancreatic insulin-producing beta-cells are selectively destroyed by the immune system in type 1 diabetes mellitus (T1DM). The autoimmune assault causes beta-cell dysfunction and death via direct contact with activated immune cells, such as macrophages and lymphocytes, and/or by exposure to soluble mediators secreted by these cells, such as pro-inflammatory cytokines, oxygen free radicals and nitric oxide (NO). The cytokines interleukin (IL)-1β, interferon (IFN)-γ and tumor necrosis factor (TNF)-α induce beta-cell death mainly by apoptosis in rodent and human islets of Langerhans [1]. Beta-cell apoptosis is a complex and highly regulated process that depends on the expression of a la