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Changes in transcriptome of native nasal epithelium expressing F508del-CFTR and intersecting data from comparable studies

Luka A Clarke1*, Lisete Sousa2, Celeste Barreto3 and Margarida D Amaral1

Author Affiliations

1 BioFIG - Centre for Biodiversity, Functional and Integrative Genomics; FCUL -Faculty of Sciences, University of Lisboa, Lisboa, 1749-016, Portugal

2 CEAUL - Centre of Statistics and Applications; FCUL - Faculty of Sciences, University of Lisboa, Lisboa, 1749-016, Portugal

3 Department of Pediatrics, Hospital de Santa Maria, Avenida Professor Egas Moniz, Lisboa, 1649-035, Portugal

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Respiratory Research 2013, 14:38  doi:10.1186/1465-9921-14-38

Published: 28 March 2013

Abstract

Background

Microarray studies related to cystic fibrosis (CF) airway gene expression have gone some way in clarifying the complex molecular background of CF lung diseases, but have made little progress in defining a robust “molecular signature” associated with mutant CFTR expression. Disparate methodological and statistical analyses complicate comparisons between independent studies of the CF transcriptome, and although each study may be valid in isolation, the conclusions reached differ widely.

Methods

We carried out a small-scale whole genome microarray study of gene expression in human native nasal epithelial cells from F508del-CFTR homozygotes in comparison to non-CF controls. We performed superficial comparisons with other microarray datasets in an attempt to identify a subset of regulated genes that could act as a signature of F508del-CFTR expression in native airway tissue samples.

Results

Among the alterations detected in CF, up-regulation of genes involved in cell proliferation, and down-regulation of cilia genes were the most notable. Other changes involved gene expression changes in calcium and membrane pathways, inflammation, defence response, wound healing and the involvement of estrogen signalling. Comparison of our data set with previously published studies allowed us to assess the consistency of independent microarray data sets, and shed light on the limitations of such snapshot studies in measuring a system as subtle and dynamic as the transcriptome. Comparison of in-vivo studies nevertheless yielded a small molecular CF signature worthy of future investigation.

Conclusions

Despite the variability among the independent studies, the current CF transcriptome meta-analysis identified subsets of differentially expressed genes in native airway tissues which provide both interesting clues to CF pathogenesis and a possible CF biomarker.