Disruption of normal patterns of FOXF1 expression in a lethal disorder of lung development

Abstract

BackgroundAlveolar capillary dysplasia with misalignment of the pulmonary veins (ACDMPV) is a lethal disorder of lung development. ACDMPV is associated with haploinsufficiency of the transcription factor FOXF1, which plays an important role in the development of the lung and intestine. CNVs upstream of the FOXF1 gene have also been associated with an ACDMPV phenotype, but mechanism(s) by which these deletions disrupt lung development are not well understood. The objective of our study is to gain insights into the mechanisms by which CNVs contribute to an ACDMPV phenotype.MethodsWe analysed primary lung tissue from an infant with classic clinical and histological findings of ACDMPV and harboured a 340 kb deletion on chromosome 16q24.1 located 250 kb upstream of FOXF1.ResultsIn RNA generated from paraffin-fixed lung sections, our patient had lower expression of FOXF1 than age-matched controls. He also had an abnormal pattern of FOXF1 protein expression, with a dramatic loss of FOXF1 expression in the lung. To gain insights into the mechanisms underlying these changes, we assessed the epigenetic landscape using chromatin immunoprecipitation, which demonstrated loss of histone H3 lysine 27 acetylation (H3K27Ac), an epigenetic mark of active enhancers, in the region of the deletion.ConclusionsTogether, these data suggest that the deletion disrupts an enhancer responsible for directing FOXF1 expression in the developing lung and provide novel insights into the mechanisms underlying a fatal developmental lung disorder.

Application of second-generation sequencing in congenital pulmonary airway malformations

“…Rawlins EL 38 found that FOXJ1 is progressively expressed in ciliated cells during lung development and that when FOXJ1 is fully expressed in ciliated cell precursors, the cells stop proliferating or have a significantly longer division cycle. Differential expression analysis in this group of samples revealed high FOXJ1 expression ( P = 0.00024), and GO functional enrichment analysis suggested that FOXJ1 is involved in various aspects of respiratory differentiation, respiratory epithelial cells, ciliary cell differentiation, cilia assembly and motility 39 .…”

Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus

“…However, lung tissue contains a heterogeneous cell population and thus, the DMRs identified are not cell type specific. In human and mice lung tissue, FOXF1 is mainly expressed in mesenchymal, smooth muscle and endothelial cells [47,[49][50][51]. To study whether aberrant methylation of the FOXF1 locus is specific for one of these cell types, it would be interesting to study DNA methylation patterns in sorted cells from fresh ACD/MPV lung tissues.…”

The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues

“…However, this seems not to be the case, since genomic annotations of H3K27ac obtained by EPAT-ChIP were found to overlap with those produced by other research groups (e.g., ChIP-seq from ENCODE) [24]. To date, PAT-ChIP has been applied by different research groups to locus-specific and genome-wide studies, supporting the reproducibility of the entire procedure [31][32][33][34][35][36][37][38][39][40][41][42][43]. Notably, the last 2 years have seen the birth of three other procedures.…”