Gene expression profiling reveals differential patterns between microcystic congenital cystic adenomatoid malformation and congenital lobar emphysema

Introduction: Congenital cystic adenomatoid malformation (CCAM), especially type-III, shares similar sonographic features with congenital lobar emphysema (CLE) in routine ultrasound scan. Thus, prenatal differentiation of CLE from a microcystic CCAM is challenging and difficult in practice. Discovery of molecular biomarkers has important clinical significance.

Methods: We profiled gene expression in lung tissue from four CCAM type-III and five CLE subjects by microarray. A bioinformatic tool was used for signal pathways enrichment analysis. Further, quantitative reverse transcriptase PCR (qRT-PCR) was used to verify the results.

Results: A total of 426 genes were identified to be significantly differentially expressed (fold-change >2.0, q value <0.05) between microcystic CCAM and CLE. Of these differentially expressed genes (DEGs), 392 were upregulated and 34 were downregulated in microcystic CCAM compared with CLE. Unsupervised clustering of the "expressed" genes could clearly delineate the CCAM and CLE samples. We also confirmed that eight randomly chose genes were differentially expressed at the mRNA level between CCAM and CLE.

Conclusions: CCAM type-III and CLE have differential gene expression patterns. Our pilot study may gain a deeper understanding of the organogenetic origins and pathogenesis of these conditions. The suggestive candidates may serve as potential biomarkers for definitive diagnosis of congenital cystic lung lesions and eventually to treat them appropriately.