Novel FOXF1 Deep Intronic Deletion Causes Lethal Lung Developmental Disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins

ABSTRACT Haploinsufficiency of FOXF1 causes an autosomal dominant neonatally lethal lung disorder, alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV). We identified novel 0.8‐kb deletion within the 1.4‐kb intron of FOXF1 in a deceased newborn diagnosed with ACDMPV. The deletion arose de novo on the maternal copy of the chromosome 16, and did not affect FOXF1 minigene splicing tested in lung fibroblasts. However, FOXF1 transcript level in the ACDMPV peripheral lung tissue was reduced by almost 40%. We found that, in an in vitro reporter assay, the FOXF1 intron exhibited moderate transcriptional enhancer activity, correlating with the presence of binding sites for expression regulators CTCF and CEBPB, whereas its truncated copy, which lost major CTCF and CEBPB‐binding sites, inhibited the FOXF1 promoter. Our data further emphasize the importance of testing the non‐protein coding regions of the genome currently not covered by diagnostic chromosomal microarray analyses or whole‐exome sequencing. Haploinsufficiency of FOXF1 causes neonatal lethal Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACDMPV). We report a novel pathogenic FOXF1 deep intronic deletion that did not affect major splicing sites. Results of the in vitro minigene‐based splicing and reporter assays performed in normal fetal lung fibroblasts suggest that the deletion likely compromised the intronic element(s) apparently regulating FOXF1 transcription. Our data further emphasize the importance of inclusion of non‐coding regions of the human genome in diagnostic testing.