Control of the proinflammatory state in cystic fibrosis lung epithelial cells by genes from the TNF-alpha R/NF kappa B pathway

Background: Cystic fibrosis (CF) is the most common, lethal autosomal reces sive disease affecting children in the United States and Europe. Extensive work is being performed to develop both gene and drug therapies. The princi pal mutation causing CF is in the CFTR gene ([Delta F508]CFTR). This mutati on causes the mutant protein to traffic poorly to the plasma membrane, and degrades CFTR chloride channel activity. CPX, a candidate drug for CF, bind s to mutant CFTR and corrects the trafficking deficit. CPX also activates m utant CFTR chloride channel activity. CF airways are phenotypically inundat ed by inflammatory signals, primarily contributed by sustained secretion of the proinflammatory cytokine interleukin 8 (IL-8) from mutant CFTR airway epithelial cells. IL-8 production is controlled by genes from the TNF-alpha R/NF kappaB pathway, and it is possible that the CF phenotype is due to dys function of genes from this pathway. In addition, because drug therapy with CPX and gene therapy with CFTR have the same common endpoint of raising th e levels of CFTR, we have hypothesized that either approach should have a c ommon genomic endpoint. Materials and Methods: To test this hypothesis, we studied IL-8 secretion a nd global gene expression in IB-3 CF lung epithelial cells. The cells were treated by either gene therapy with wild-type CFTR, or by pharmacotherapy w ith the CFTR-surrogate drug CPX. CF cells, treated with either CFTR or CPX, were also exposed to Pseudomonas aeruginosa, a common chronic pathogen in CF patients. cDNA microarrays were used to assess global gene expression un der the different conditions. A novel bioinformatic algorithm (GENESAVER) w as developed to identify genes whose expression paralleled secretion of IL- 8. Results: We report here that IB3 CF cells secrete massive levels of IL-8. H owever, both gene therapy with CFTR and drug therapy with CPX substantially suppress IL-8 secretion. Nonetheless, both gene and drug therapy allow the CF cells to respond with physiologic secretion of IL-8 when the cells are exposed to P. aeruginosa. Thus, neither CFTR nor CPX acts as a nonspecific suppressor of IL-8 secretion from CF cells. Consistently, pharmacogenomic a nalysis indicates that CF cells treated with CPX greatly resemble CF cells treated with CFTR by gene therapy. Additionally, the same result obtains in the presence of P. aeruginosa. Classical hierarchical cluster analysis, ba sed on similarity of global gene expression, also supports this conclusion. The GENESAVER algorithm, using the IL-8 secretion level as a physiologic v ariable, identifies a subset of genes from the TNF-alphaR/NF kappaB pathway that is expressed in phase with IL-8 secretion from CF epithelial cells. C ertain other genes, previously known to be positively associated with CF al so fall into this category. Identified genes known to code for known inhibi tors are expressed inversely, out of phase with IL-8 secretion. Conclusions: Wild-type CFTR and CPX both suppress proinflammatory IL-8 secr etion from CF epithelial cells. The mechanism, as defined by pharmacogenomi c analysis, involves identified genes from the TNF-alphaR/NF kappaB pathway . The close relationship between IL-8 secretion and genes from the TNF-alph aR/NF kappaB pathway suggests that molecular or pharmaceutical targeting of these novel genes may have strategic use in the development of new therapi es for CF. From the perspective of global gene expression, both gene and dr ug therapy have similar genomic consequences. This is the first example sho wing equivalence of gene and drug therapy in CF, and suggests that a gene t herapy-defined endpoint may prove to be a powerful paradigm for CF drug dis covery. Finally, because the GENESAVER algorithm is capable of isolating di sease-relevant genes in a hypothesis-driven manner without recourse to any a priori knowledge about the system, this new algorithm may also prove usef ul in applications to other genetic diseases.