Host Microarray Molecular Signature and Serologic Evaluation of Stages of Pseudomonas aeruginosa Infection in Cystic Fibrosis

Abstract

Background: Cystic fibrosis (CF) is a genetic disorder caused by mutations in the CF transmembrane regulator gene (CFTR); lung disease is characterized by chronic infection by Pseudomonas aeruginosa, the major cause of morbidity and mortality in patients with CF. However, oropharyngeal cultures for P. aeruginosa in young children result in poor specificity for lower airway infection. We used a novel approach to generate genomewide expression profiles to identify markers for P. aeruginosa infection and CF disease severity. Transcription was induced in healthy unrelated peripheral blood mononuclear cells through coculture with autologous serum (self-baseline control), allogeneic serums (healthy unrelated controls), and serums from patients with CF. Methodology: All CF diagnoses included sweat chloride levels greater than or equal to 60 mEq/L and/or two CFTR mutations. We performed various ELISAs against 192 serum samples (43 individuals sampled over 15 years) and comparative cultures. Concurrently, we completed expression profiling of RNA (HU133 plus 2.0 array; Affymetrix, Santa Clara, CA) from coculture of peripheral blood mononuclear cells with the serum of patients with CF, who possessed increasing degrees of colonization with P. aeruginosa. Differentially expressed probe sets were defined as those possessing a false discovery rate less than 10% and |log2 ratio| greater than 0.5 among comparison groups. Results: Our ELISA data indicated that the host response to P. aeruginosa infection increased over time, suggesting that serology to P. aeruginosa may help determine initial airway pathology. Comparison of array signatures performed before and after seroconversion identified several hundred unique genes; the most significant differences in gene expression included host genes involved with airway defense, antigen presentation, and transcription. Conclusions: Our methodology consistently identified a small number of genes that were unique to patients with CF or to patients with CF with initial P. aeruginosa infection conversion. These genes merit investigation as active participants in the function of the lung microbiome and may serve as therapeutic targets for P. aeruginosa infection in CF.